Methods and processes for non-invasive assessment of genetic variations

ABSTRACT

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

RELATED APPLICATIONS

This patent application is a continuation of U.S. patent applicationSer. No. 13/782,901 filed on Mar. 1, 2013, entitled METHODS ANDPROCESSES FOR NON-INVASIVE ASSESSMENT OF GENETIC VARIATIONS, namingCharles R. Cantor, Grace DeSantis, Reinhold Mueller, and Mathias Ehrichas inventors, and designated by Attorney Docket No. SEQ-6039-UT, whichclaims the benefit of U.S. Provisional Patent Application No. 61/606,226filed on Mar. 2, 2012, entitled METHODS AND PROCESSES FOR NON-INVASIVEASSESSMENT OF GENETIC VARIATIONS, naming Charles R. Cantor as inventor,and designated by Attorney Docket No. SEQ-6039-PV. The entire content ofthe foregoing applications are incorporated herein by reference,including all text, tables and drawings.

FIELD

Technology provided herein relates in part to methods, processes andapparatuses for non-invasive assessment of genetic variations.

BACKGROUND

Genetic information of living organisms (e.g., animals, plants andmicroorganisms) and other forms of replicating genetic information(e.g., viruses) is encoded in deoxyribonucleic acid (DNA) or ribonucleicacid (RNA). Genetic information is a succession of nucleotides ormodified nucleotides representing the primary structure of chemical orhypothetical nucleic acids. In humans, the complete genome containsabout 30,000 genes located on twenty-four (24) chromosomes (see TheHuman Genome, T. Strachan, BIOS Scientific Publishers, 1992). Each geneencodes a specific protein, which after expression via transcription andtranslation fulfills a specific biochemical function within a livingcell.

Many medical conditions are caused by one or more genetic variations.Certain genetic variations cause medical conditions that include, forexample, hemophilia, thalassemia, Duchenne Muscular Dystrophy (DMD),Huntington's Disease (HD), Alzheimer's Disease and Cystic Fibrosis (CF)(Human Genome Mutations, D. N. Cooper and M. Krawczak, BIOS Publishers,1993). Such genetic diseases can result from an addition, substitution,or deletion of a single nucleotide in DNA of a particular gene. Certainbirth defects are caused by a chromosomal abnormality, also referred toas an aneuploidy, such as Trisomy 21 (Down's Syndrome), Trisomy 13(Patau Syndrome), Trisomy 18 (Edward's Syndrome), Monosomy X (Turner'sSyndrome) and certain sex chromosome aneuploidies such as Klinefelter'sSyndrome (XXY), for example. Another genetic variation is fetal gender,which can often be determined based on sex chromosomes X and Y. Somegenetic variations may predispose an individual to, or cause, any of anumber of diseases such as, for example, diabetes, arteriosclerosis,obesity, various autoimmune diseases and cancer (e.g., colorectal,breast, ovarian, lung).

Identifying one or more genetic variations or variances can lead todiagnosis of, or determining predisposition to, a particular medicalcondition. Identifying a genetic variance can result in facilitating amedical decision and/or employing a helpful medical procedure.Identification of one or more genetic variations or variances sometimesinvolves the analysis of cell-free DNA.

Cell-free DNA (CF-DNA) is composed of DNA fragments that originate fromcell death and circulate in peripheral blood. High concentrations ofCF-DNA can be indicative of certain clinical conditions such as cancer,trauma, burns, myocardial infarction, stroke, sepsis, infection, andother illnesses. Additionally, cell-free fetal DNA (CFF-DNA) can bedetected in the maternal bloodstream and used for various noninvasiveprenatal diagnostics.

The presence of fetal nucleic acid in maternal plasma allows fornon-invasive prenatal diagnosis through the analysis of a maternal bloodsample. For example, quantitative abnormalities of fetal DNA in maternalplasma can be associated with a number of pregnancy-associateddisorders, including preeclampsia, preterm labor, antepartum hemorrhage,invasive placentation, fetal Down syndrome, and other fetal chromosomalaneuploidies. Hence, fetal nucleic acid analysis in maternal plasma canbe a useful mechanism for the monitoring of fetomaternal well-being.

Early detection of pregnancy-related conditions, including complicationsduring pregnancy and genetic defects of the fetus is important, as itallows early medical intervention necessary for the safety of both themother and the fetus. Prenatal diagnosis traditionally has beenconducted using cells isolated from the fetus through procedures such aschorionic villus sampling (CVS) or amniocentesis. However, theseconventional methods are invasive and present an appreciable risk toboth the mother and the fetus. The National Health Service currentlycites a miscarriage rate of between 1 and 2 percent following theinvasive amniocentesis and chorionic villus sampling (CVS) tests. Theuse of non-invasive screening techniques that utilize circulatingCFF-DNA can be an alternative to these invasive approaches.

SUMMARY

Provided in some aspects are methods for enriching fetal nucleic acid insample nucleic acid that includes fetal nucleic acid and maternalnucleic acid, comprising: (a) obtaining cell-free circulating samplenucleic acid from a biological sample from a pregnant female, whichsample nucleic acid comprises vesicle-free nucleic acid and vesicularnucleic acid; and (b) separating some or substantially all of thevesicular nucleic acid from the sample nucleic acid, thereby generatinga separation product enriched for the vesicle-free nucleic acid, wherefetal nucleic acid in the separation product is enriched relative tofetal nucleic acid in the sample nucleic acid. In some embodiments, themethod further comprises (c) analyzing nucleic acid in the separationproduct.

Also provided, in some aspects, are methods which comprise analyzingnucleic acid in a separation product prepared by a process comprising:(a) obtaining cell-free circulating sample nucleic acid from abiological sample from a pregnant female, which sample nucleic acidcomprises vesicle-free nucleic acid, vesicular nucleic acid, maternalnucleic acid and fetal nucleic acid; and (b) separating some orsubstantially all of the vesicular nucleic acid from the sample nucleicacid, thereby generating a separation product enriched for thevesicle-free nucleic acid, where the fetal nucleic acid in theseparation product is enriched relative to the fetal nucleic acid in thesample nucleic acid.

Also provided, in some aspects, are methods for enriching vesicle-freenucleic acid in sample nucleic acid, comprising: (a) obtaining cell-freecirculating sample nucleic acid from a biological sample, which samplenucleic acid comprises vesicle-free nucleic acid and vesicular nucleicacid; and (b) separating some or substantially all of the vesicularnucleic acid from the sample nucleic acid, thereby generating aseparation product, where vesicle-free nucleic acid in the separationproduct is enriched relative to vesicle-free nucleic acid in the samplenucleic acid. In some embodiments, the method further comprises (c)analyzing nucleic acid in the separation product.

Also provided, in some aspects, are methods which comprise analyzingnucleic acid in a separation product prepared by a process comprising:(a) obtaining cell-free circulating sample nucleic acid from abiological sample, which sample nucleic acid comprises vesicle-freenucleic acid and vesicular nucleic acid; and (b) separating some orsubstantially all of the vesicular nucleic acid from the sample nucleicacid, thereby generating a separation product, where vesicle-freenucleic acid in the separation product is enriched relative tovesicle-free nucleic acid in the sample nucleic acid.

Also provided, in some aspects, are methods for enriching fetal nucleicacid in sample nucleic acid that includes fetal nucleic acid andmaternal nucleic acid, comprising (a) obtaining cell-free circulatingsample nucleic acid from a biological sample from a pregnant female,which sample nucleic acid comprises maternal-derived vesicular nucleicacid and fetal-derived vesicular nucleic acid; and (b) separating someor substantially all of the maternal-derived vesicular nucleic acid fromthe fetal-derived vesicular nucleic acid, thereby generating aseparation product enriched for the fetal-derived vesicular nucleicacid, where fetal nucleic acid in the separation product is enrichedrelative to fetal nucleic acid in the sample nucleic acid.

Also provided, in some aspects, are methods for enriching fetal nucleicacid in sample nucleic acid that includes fetal nucleic acid andmaternal nucleic acid, comprising (a) obtaining cell-free circulatingsample nucleic acid from a biological sample from a pregnant female,which sample nucleic acid comprises vesicle-free nucleic acid andvesicular nucleic acid; and (b) separating some or substantially all ofthe vesicular nucleic acid from the sample nucleic acid, therebygenerating a separation product enriched for the vesicular nucleic acid,where fetal nucleic acid in the separation product is enriched relativeto fetal nucleic acid in the sample nucleic acid.

In some embodiments, separating some or substantially all of thematernal-derived vesicular nucleic acid from the fetal-derived vesicularnucleic acid comprises contacting the sample nucleic acid with an agentthat specifically binds to maternal-derived vesicular nucleic acid. Insome embodiments, separating some or substantially all of thematernal-derived vesicular nucleic acid from the fetal-derived vesicularnucleic acid comprises contacting the sample nucleic acid with an agentthat specifically binds to fetal-derived vesicular nucleic acid.

In some embodiments, separating some or substantially all of thevesicular nucleic acid from the sample nucleic acid comprises filteringthe sample nucleic acid and sometimes comprises centrifuging the samplenucleic acid and sometimes comprises use of ultracentrifugation. In someembodiments, separating some or substantially all of the vesicularnucleic acid from the sample nucleic acid comprises contacting thesample nucleic acid with an agent that specifically binds to vesiclescomprising the vesicular nucleic acid. In some embodiments, the agent isan antibody. In some embodiments, the agent specifically binds tovesicles from hemopoietic tissue. In some embodiments, the agentspecifically binds to vesicles from red blood cells. In some instances,the agent specifically binds to CD235a. In some embodiments, the agentspecifically binds to vesicles from leukocytes. In some instances, theagent specifically binds to CD45. In some embodiments, the agentspecifically binds to vesicles from lymphocytes. In some instances, theagent specifically binds to a vesicular component chosen from CD4, CD8and CD20. In some embodiments, the agent specifically binds to vesiclesfrom granulocytes. In some instances, the agent specifically binds toCD66b. In some embodiments, the agent specifically binds to vesiclesfrom monocytes. In some instances, the agent specifically binds to CD14.In some embodiments, the agent specifically binds to vesicles fromplatelets. In some instances, the agent specifically binds to avesicular component chosen from CD31, CD41, CD41a, CD42a, CD42b, CD61and CD62P. In some embodiments, the agent specifically binds to vesiclesfrom endothelial cells. In some instances, the agent specifically bindsto a vesicular component chosen from CD31, CD34, CD54, CD62E, CD51,CD105, CD106, CD144 and CD146.

In some embodiments, generating the separation product comprisesseparating components bound by the agent away from the sample nucleicacid. In some embodiments, separating some or substantially all of thevesicular nucleic acid from the sample nucleic acid further comprisescontacting the sample nucleic acid with an agent that specifically bindsto a histone associated with vesicle-free nucleic acid. In someinstances, the agent specifically binds to histone H3.3. In someinstances, the agent specifically binds to histone H1. In someinstances, histone H1 is unmethylated.

In some embodiments, the vesicular nucleic acid is within a vesiclehaving a diameter of less than about 1 micrometer. In some instances,the diameter is about 10 nanometers to about 600 nanometers. In someinstances, the diameter is about 40 nanometers to about 100 nanometers.

Also provided, in some aspects, are methods for enriching fetal nucleicacid in sample nucleic acid that includes fetal nucleic acid andmaternal nucleic acid, comprising: (a) obtaining cell-free circulatingsample nucleic acid from a biological sample from a pregnant female,which sample nucleic acid comprises a first histone-associated nucleicacid species and a second histone-associated nucleic acid species; and(b) separating some or substantially all of the first histone-associatednucleic acid species from the sample nucleic acid, thereby generating aseparation product enriched for the second histone-associated nucleicacid species, where fetal nucleic acid in the separation product isenriched relative to fetal nucleic acid in the sample nucleic acid. Insome embodiments, the method further comprises (c) analyzing nucleicacid in the separation product.

Also provided, in some aspects, are methods which comprise analyzingnucleic acid in a separation product prepared by a process comprising:(a) obtaining cell-free circulating sample nucleic acid from abiological sample from a pregnant female, which sample nucleic acidcomprises a first histone-associated nucleic acid species, a secondhistone-associated nucleic acid species, maternal nucleic acid and fetalnucleic acid; and (b) separating some or substantially all of the firsthistone-associated nucleic acid species from the sample nucleic acid,thereby generating a separation product enriched for the secondhistone-associated nucleic acid species, where the fetal nucleic acid inthe separation product is enriched relative to the fetal nucleic acid inthe sample nucleic acid.

Also provided, in some aspects, are methods for enriching ahistone-associated nucleic acid species in sample nucleic acid,comprising: (a) obtaining cell-free circulating sample nucleic acid froma biological sample, which sample nucleic acid comprises a firsthistone-associated nucleic acid species and a second histone-associatednucleic acid species; and (b) separating some or substantially all ofthe first histone-associated nucleic acid species from the samplenucleic acid, thereby generating a separation product enriched for thesecond histone-associated nucleic acid species. In some embodiments, themethod further comprises (c) analyzing nucleic acid in the separationproduct.

Also provided, in some aspects, are methods which comprise analyzingnucleic acid in a separation product prepared by a process comprising:(a) obtaining cell-free circulating sample nucleic acid from abiological sample, which sample nucleic acid comprises a firsthistone-associated nucleic acid species and a second histone-associatednucleic acid species; and (b) separating some or substantially all ofthe first histone-associated nucleic acid species from the samplenucleic acid, thereby generating a separation product enriched for thesecond histone-associated nucleic acid species.

Also provided, in some aspects, are methods for enriching fetal nucleicacid in sample nucleic acid that includes fetal nucleic acid andmaternal nucleic acid, comprising (a) obtaining cell-free circulatingsample nucleic acid from a biological sample from a pregnant female,which sample nucleic acid comprises a first histone-associated nucleicacid species and a second histone-associated nucleic acid species; and(b) separating some or substantially all of the first histone-associatednucleic acid species from the second histone-associated nucleic acidspecies, thereby generating a separation product enriched for the secondhistone-associated nucleic acid species, where fetal nucleic acid in theseparation product is enriched relative to fetal nucleic acid in thesample nucleic acid.

In some embodiments, a method comprises (c) analyzing nucleic acid inthe separation product. In some embodiments, separating some orsubstantially all of the first histone-associated nucleic acid speciesfrom the second histone-associated nucleic acid species comprisescontacting the sample nucleic acid with an agent that specifically bindsto a histone associated with the first histone-associated nucleic acidspecies. In some embodiments, separating some or substantially all ofthe first histone-associated nucleic acid species from the secondhistone-associated nucleic acid species comprises contacting the samplenucleic acid with an agent that specifically binds to a histoneassociated with the second histone-associated nucleic acid species.

In some embodiments, the agent specifically binds to histone H1. In someembodiments, the agent specifically binds to histone H1.0. In someembodiments, the agent specifically binds to histone H1.1. In someembodiments, the agent specifically binds to histone H1.3. In someembodiments, the agent specifically binds to histone H1.5. In someembodiments, the agent is an antibody.

In some embodiments, the method comprises lysing vesicles present in thesample nucleic acid. In some embodiments, separating some orsubstantially all of the first histone-associated nucleic acid speciesfrom the sample nucleic acid comprises contacting the sample nucleicacid with an agent that specifically binds to a histone associated withthe first histone-associated nucleic acid species. In some embodiments,the agent is an antibody. In some embodiments, the agent specificallybinds to histone H3.3. In some instances, the agent specifically bindsto histone H1. In some instances, the histone H1 is unmethylated. Insome embodiments, generating the separation product comprises separatingcomponents bound by the agent away from the sample nucleic acid.

In some embodiments, the sample nucleic acid is from blood plasma, andin some embodiments, the sample nucleic acid is from blood serum. Insome embodiments, obtaining the sample nucleic acid comprises subjectingthe biological sample to an in vitro process that isolates the samplenucleic acid from other sample components. In some instances, theseparation product comprises about 50% or greater vesicle-free nucleicacid. In some instances, the separation product comprises about 50% orgreater second histone-associated nucleic acid species. In someembodiments, analyzing the nucleic acid in the separation productcomprises subjecting the nucleic acid to an in vitro sequencing process.In some embodiments, the sequencing process provides sequence reads. Insome embodiments, the method comprises mapping the sequence reads to areference sequence and sometimes comprises counting the sequence readsmapped to the reference sequence. In some embodiments, the methodcomprises utilizing the counted sequence reads to generate an outcomedeterminative of the presence or absence of a genetic variation. In someembodiments, the genetic variation is a copy number variation. In someembodiments, the genetic variation is a chromosome aneuploidy andsometimes is a chromosome 21 aneuploidy.

Certain aspects of the technology are described further in the followingdescription, examples, drawings and claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The drawings illustrate aspects of the technology and are not limiting.For clarity and ease of illustration, the drawings are not made to scaleand, in some instances, various aspects may be shown exaggerated orenlarged to facilitate an understanding of particular embodiments.

FIG. 1 shows a centrifugation diagram.

FIG. 2 shows fetal copy numbers obtained for certain centrifugationconditions.

FIG. 3 shows total copy numbers obtained for certain centrifugationconditions.

FIG. 4 shows fetal fractions obtained for certain centrifugationconditions.

FIG. 5 presents a table showing a distribution of circulating DNA.

FIG. 6 presents a table showing a distribution of circulating DNA.

DETAILED DESCRIPTION

Provided herein are methods for enriching a sub-population of cell-freenucleic acid from a larger pool of cell-free nucleic acid in a samplenucleic acid. Cell-free nucleic acid often comprises a mixture of freenucleic acid fragments and nucleic acid fragments associated withvarious cellular components and/or cellular remnants, such as vesicles.In certain instances, it is advantageous to separate nucleic acidfragments associated with certain cellular components/remnants from thefree (e.g., vesicle-free) nucleic acid fragments. In certain instances,it is advantageous to separate nucleic acid fragments associated withcertain cellular components/remnants from nucleic acid fragmentsassociated with different cellular components/remnants. Cell-freenucleic acid often is present in nucleosome form, and varioussubpopulations of nucleosomal cell-free nucleic acid can be associatedwith certain histones or histone variants. In certain instances, it isadvantageous to separate a subpopulation of cell-free nucleic acidassociated with a particular histone or histone variant from the samplenucleic acid. Such separation methods can be useful for the enrichmentof a particular subpopulation of cell-free nucleic acid. Provided hereinare methods for enriching vesicle-free nucleic acid, vesicular nucleicacid and/or a histone-associated nucleic acid species in a samplecomprising circulating cell-free nucleic acid.

Provided also are improved methods, processes and apparatuses useful foridentifying genetic variations. Identifying one or more geneticvariations or variances can lead to diagnosis of, or determiningpredisposition to, a particular medical condition. Identifying a geneticvariance can result in facilitating a medical decision and/or employinga helpful medical procedure.

Provided also are methods, processes and apparatuses useful foridentifying a genetic variation. Identifying a genetic variationsometimes comprises detecting a copy number variation and/or sometimescomprises adjusting an elevation comprising a copy number variation. Insome embodiments, identifying a genetic variation by a method describedherein can lead to a diagnosis of, or determining a predisposition to, aparticular medical condition. Identifying a genetic variance can resultin facilitating a medical decision and/or employing a helpful medicalprocedure.

Samples

Provided herein are methods and compositions for analyzing nucleic acid.In some embodiments, nucleic acid fragments in a mixture of nucleic acidfragments are analyzed. A mixture of nucleic acids can comprise two ormore nucleic acid fragment species having different nucleotidesequences, different fragment lengths, different origins (e.g., genomicorigins, fetal vs. maternal origins, cell or tissue origins, sampleorigins, subject origins, and the like), or combinations thereof.

Nucleic acid or a nucleic acid mixture utilized in methods andapparatuses described herein often is isolated from a sample obtainedfrom a subject. A subject can be any living or non-living organism,including but not limited to a human, a non-human animal, a plant, abacterium, a fungus or a protist. Any human or non-human animal can beselected, including but not limited to mammal, reptile, avian,amphibian, fish, ungulate, ruminant, bovine (e.g., cattle), equine(e.g., horse), caprine and ovine (e.g., sheep, goat), swine (e.g., pig),camelid (e.g., camel, llama, alpaca), monkey, ape (e.g., gorilla,chimpanzee), ursid (e.g., bear), poultry, dog, cat, mouse, rat, fish,dolphin, whale and shark. A subject may be a male or female (e.g.,woman).

Nucleic acid may be isolated from any type of suitable biologicalspecimen or sample (e.g., a test sample). A sample or test sample can beany specimen that is isolated or obtained from a subject (e.g., a humansubject, a pregnant female). Non-limiting examples of specimens includefluid or tissue from a subject, including, without limitation, umbilicalcord blood, chorionic villi, amniotic fluid, cerebrospinal fluid, spinalfluid, lavage fluid (e.g., bronchoalveolar, gastric, peritoneal, ductal,ear, arthroscopic), biopsy sample (e.g., from pre-implantation embryo),celocentesis sample, fetal nucleated cells or fetal cellular remnants,washings of female reproductive tract, urine, feces, sputum, saliva,nasal mucous, prostate fluid, lavage, semen, lymphatic fluid, bile,tears, sweat, breast milk, breast fluid, embryonic cells and fetal cells(e.g. placental cells). In some embodiments, a biological sample is acervical swab from a subject. In some embodiments, a biological samplemay be blood and sometimes plasma or serum. As used herein, the term“blood” encompasses whole blood or any fractions of blood, such as serumand plasma as conventionally defined, for example. Blood or fractionsthereof often comprise nucleosomes (e.g., maternal and/or fetalnucleosomes). Nucleosomes comprise nucleic acids and are sometimescell-free or intracellular. Blood also comprises buffy coats. Buffycoats are sometimes isolated by utilizing a ficoll gradient. Buffy coatscan comprise white blood cells (e.g., leukocytes, T-cells, B-cells,platelets, and the like). In certain instances, buffy coats comprisematernal and/or fetal nucleic acid. Blood plasma refers to the fractionof whole blood resulting from centrifugation of blood treated withanticoagulants. Blood serum refers to the watery portion of fluidremaining after a blood sample has coagulated. Fluid or tissue samplesoften are collected in accordance with standard protocols hospitals orclinics generally follow. For blood, an appropriate amount of peripheralblood (e.g., between 3-40 milliliters) often is collected and can bestored according to standard procedures prior to or after preparation. Afluid or tissue sample from which nucleic acid is extracted may beacellular (e.g., cell-free). In some embodiments, a fluid or tissuesample may contain cellular elements or cellular remnants. In someembodiments fetal cells or cancer cells may be included in the sample.

A sample often is heterogeneous, by which is meant that more than onetype of nucleic acid species is present in the sample. For example,heterogeneous nucleic acid can include, but is not limited to, (i) fetalderived and maternal derived nucleic acid, (ii) cancer and non-cancernucleic acid, (iii) pathogen and host nucleic acid, and more generally,(iv) mutated and wild-type nucleic acid. A sample may be heterogeneousbecause more than one cell type is present, such as a fetal cell and amaternal cell, a cancer and non-cancer cell, or a pathogenic and hostcell. In some embodiments, a minority nucleic acid species and amajority nucleic acid species is present.

For prenatal applications of technology described herein, fluid ortissue sample may be collected from a female at a gestational agesuitable for testing, or from a female who is being tested for possiblepregnancy. Suitable gestational age may vary depending on the prenataltest being performed. In certain embodiments, a pregnant female subjectsometimes is in the first trimester of pregnancy, at times in the secondtrimester of pregnancy, or sometimes in the third trimester ofpregnancy. In certain embodiments, a fluid or tissue is collected from apregnant female between about 1 to about 45 weeks of fetal gestation(e.g., at 1-4, 4-8, 8-12, 12-16, 16-20, 20-24, 24-28, 28-32, 32-36,36-40 or 40-44 weeks of fetal gestation), and sometimes between about 5to about 28 weeks of fetal gestation (e.g., at 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 or 27 weeks offetal gestation). In some embodiments, a fluid or tissue sample iscollected from a pregnant female during or just after (e.g., 0 to 72hours after) giving birth (e.g., vaginal or non-vaginal birth (e.g.,surgical delivery)).

Nucleic Acid Isolation and Processing

Nucleic acid may be derived from one or more sources (e.g., cells,serum, plasma, buffy coat, lymphatic fluid, skin, soil, and the like) bymethods known in the art. Cell lysis procedures and reagents are knownin the art and may generally be performed by chemical (e.g., detergent,hypotonic solutions, enzymatic procedures, and the like, or combinationthereof), physical (e.g., French press, sonication, and the like), orelectrolytic lysis methods. Any suitable lysis procedure can beutilized. For example, chemical methods generally employ lysing agentsto disrupt cells and extract the nucleic acids from the cells, followedby treatment with chaotropic salts. Physical methods such as freeze/thawfollowed by grinding, the use of cell presses and the like also areuseful. High salt lysis procedures also are commonly used. For example,an alkaline lysis procedure may be utilized. The latter proceduretraditionally incorporates the use of phenol-chloroform solutions, andan alternative phenol-chloroform-free procedure involving threesolutions can be utilized. In the latter procedures, one solution cancontain 15 mM Tris, pH 8.0; 10 mM EDTA and 100 ug/ml Rnase A; a secondsolution can contain 0.2N NaOH and 1% SDS; and a third solution cancontain 3M KOAc, pH 5.5. These procedures can be found in CurrentProtocols in Molecular Biology, John Wiley & Sons, N.Y., 6.3.1-6.3.6(1989), incorporated herein in its entirety.

The terms “nucleic acid” and “nucleic acid molecule” are usedinterchangeably. The terms refer to nucleic acids of any compositionform, such as deoxyribonucleic acid (DNA, e.g., complementary DNA(cDNA), genomic DNA (gDNA) and the like), ribonucleic acid (RNA, e.g.,message RNA (mRNA), short inhibitory RNA (siRNA), ribosomal RNA (rRNA),transfer RNA (tRNA), microRNA, RNA highly expressed by the fetus orplacenta, and the like), and/or DNA or RNA analogs (e.g., containingbase analogs, sugar analogs and/or a non-native backbone and the like),RNA/DNA hybrids and polyamide nucleic acids (PNAs), all of which can bein single- or double-stranded form. Unless otherwise limited, a nucleicacid can comprise known analogs of natural nucleotides, some of whichcan function in a similar manner as naturally occurring nucleotides. Anucleic acid can be in any form useful for conducting processes herein(e.g., linear, circular, supercoiled, single-stranded, double-strandedand the like). A nucleic acid may be, or may be from, a plasmid, phage,autonomously replicating sequence (ARS), centromere, artificialchromosome, chromosome, or other nucleic acid able to replicate or bereplicated in vitro or in a host cell, a cell, a cell nucleus orcytoplasm of a cell in certain embodiments. A nucleic acid in someembodiments can be from a single chromosome or fragment thereof (e.g., anucleic acid sample may be from one chromosome of a sample obtained froma diploid organism). Nucleic acids sometimes comprise nucleosomes,fragments or parts of nucleosomes or nucleosome-like structures. Nucleicacids sometimes comprise protein (e.g., histones, DNA binding proteins,and the like). Nucleic acids analyzed by processes described hereinsometimes are substantially isolated and are not substantiallyassociated with protein or other molecules. Nucleic acids also includederivatives, variants and analogs of RNA or DNA synthesized, replicatedor amplified from single-stranded (“sense” or “antisense”, “plus” strandor “minus” strand, “forward” reading frame or “reverse” reading frame)and double-stranded polynucleotides. Deoxyribonucleotides includedeoxyadenosine, deoxycytidine, deoxyguanosine and deoxythymidine. ForRNA, the base cytosine is replaced with uracil and the sugar 2′ positionincludes a hydroxyl moiety. A nucleic acid may be prepared using anucleic acid obtained from a subject as a template.

Nucleic acid may be isolated at a different time point as compared toanother nucleic acid, where each of the samples is from the same or adifferent source. A nucleic acid may be from a nucleic acid library,such as a cDNA or RNA library, for example. A nucleic acid may be aresult of nucleic acid purification or isolation and/or amplification ofnucleic acid molecules from the sample. Nucleic acid provided forprocesses described herein may contain nucleic acid from one sample orfrom two or more samples (e.g., from 1 or more, 2 or more, 3 or more, 4or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 ormore, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 16 ormore, 17 or more, 18 or more, 19 or more, or 20 or more samples).

Nucleic acids can include extracellular nucleic acid in certainembodiments. The term “extracellular nucleic acid” as used herein canrefer to nucleic acid isolated from a source having substantially nocells and also is referred to as “cell-free” nucleic acid and/or“cell-free circulating” nucleic acid. Extracellular nucleic acid can bepresent in and obtained from blood (e.g., from the blood of a pregnantfemale). Extracellular nucleic acid often includes no detectable cellsand may contain cellular elements or cellular remnants. Non-limitingexamples of acellular sources for extracellular nucleic acid are blood,blood plasma, blood serum and urine. As used herein, the term “obtaincell-free circulating sample nucleic acid” includes obtaining a sampledirectly (e.g., collecting a sample, e.g., a test sample) or obtaining asample from another who has collected a sample. Without being limited bytheory, extracellular nucleic acid may be a product of cell apoptosisand cell breakdown, which provides basis for extracellular nucleic acidoften having a series of lengths across a spectrum (e.g., a “ladder”).

Extracellular nucleic acid can include different nucleic acid species,and therefore is referred to herein as “heterogeneous” in certainembodiments. For example, blood serum or plasma from a person havingcancer can include nucleic acid from cancer cells and nucleic acid fromnon-cancer cells. In another example, blood serum or plasma from apregnant female can include maternal nucleic acid and fetal nucleicacid. In some instances, fetal nucleic acid sometimes is about 5% toabout 50% of the overall nucleic acid (e.g., about 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,47, 48, or 49% of the total nucleic acid is fetal nucleic acid). In someembodiments, the majority of fetal nucleic acid in nucleic acid is of alength of about 500 base pairs or less (e.g., about 80, 85, 90, 91, 92,93, 94, 95, 96, 97, 98, 99 or 100% of fetal nucleic acid is of a lengthof about 500 base pairs or less). In some embodiments, the majority offetal nucleic acid in nucleic acid is of a length of about 250 basepairs or less (e.g., about 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98,99 or 100% of fetal nucleic acid is of a length of about 250 base pairsor less). In some embodiments, the majority of fetal nucleic acid innucleic acid is of a length of about 200 base pairs or less (e.g., about80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of fetal nucleicacid is of a length of about 200 base pairs or less). In someembodiments, the majority of fetal nucleic acid in nucleic acid is of alength of about 150 base pairs or less (e.g., about 80, 85, 90, 91, 92,93, 94, 95, 96, 97, 98, 99 or 100% of fetal nucleic acid is of a lengthof about 150 base pairs or less). In some embodiments, the majority offetal nucleic acid in nucleic acid is of a length of about 100 basepairs or less (e.g., about 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98,99 or 100% of fetal nucleic acid is of a length of about 100 base pairsor less). In some embodiments, the majority of fetal nucleic acid innucleic acid is of a length of about 50 base pairs or less (e.g., about80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of fetal nucleicacid is of a length of about 50 base pairs or less). In someembodiments, the majority of fetal nucleic acid in nucleic acid is of alength of about 25 base pairs or less (e.g., about 80, 85, 90, 91, 92,93, 94, 95, 96, 97, 98, 99 or 100% of fetal nucleic acid is of a lengthof about 25 base pairs or less).

Nucleic acid may be provided for conducting methods described hereinwithout processing of the sample(s) containing the nucleic acid, incertain embodiments. In some embodiments, nucleic acid is provided forconducting methods described herein after processing of the sample(s)containing the nucleic acid. For example, a nucleic acid can beextracted, isolated, purified, partially purified or amplified from thesample(s). The term “isolated” as used herein refers to nucleic acidremoved from its original environment (e.g., the natural environment ifit is naturally occurring, or a host cell if expressed exogenously), andthus is altered by human intervention (e.g., “by the hand of man”) fromits original environment. The term “isolated nucleic acid” as usedherein can refer to a nucleic acid removed from a subject (e.g., a humansubject). An isolated nucleic acid can be provided with fewernon-nucleic acid components (e.g., protein, lipid) than the amount ofcomponents present in a source sample. A composition comprising isolatednucleic acid can be about 50% to greater than 99% free of non-nucleicacid components. A composition comprising isolated nucleic acid can beabout 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater than99% free of non-nucleic acid components. The term “purified” as usedherein can refer to a nucleic acid provided that contains fewernon-nucleic acid components (e.g., protein, lipid, carbohydrate) thanthe amount of non-nucleic acid components present prior to subjectingthe nucleic acid to a purification procedure. A composition comprisingpurified nucleic acid may be about 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% orgreater than 99% free of other non-nucleic acid components. The term“purified” as used herein can refer to a nucleic acid provided thatcontains fewer nucleic acid species than in the sample source from whichthe nucleic acid is derived. A composition comprising purified nucleicacid may be about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% orgreater than 99% free of other nucleic acid species. For example, fetalnucleic acid can be purified from a mixture comprising maternal andfetal nucleic acid. In certain examples, nucleosomes comprising smallfragments of fetal nucleic acid can be purified from a mixture of largernucleosome complexes comprising larger fragments of maternal nucleicacid.

The term “amplified” as used herein refers to subjecting a targetnucleic acid in a sample to a process that linearly or exponentiallygenerates amplicon nucleic acids having the same or substantially thesame nucleotide sequence as the target nucleic acid, or segment thereof.The term “amplified” as used herein can refer to subjecting a targetnucleic acid (e.g., in a sample comprising other nucleic acids) to aprocess that selectively and linearly or exponentially generatesamplicon nucleic acids having the same or substantially the samenucleotide sequence as the target nucleic acid, or segment thereof. Theterm “amplified” as used herein can refer to subjecting a population ofnucleic acids to a process that non-selectively and linearly orexponentially generates amplicon nucleic acids having the same orsubstantially the same nucleotide sequence as nucleic acids, or portionsthereof, that were present in the sample prior to amplification. In someembodiments, the term “amplified” refers to a method that comprises apolymerase chain reaction (PCR).

Nucleic acid also may be processed by subjecting nucleic acid to amethod that generates nucleic acid fragments, in certain embodiments,before providing nucleic acid for a process described herein. In someembodiments, nucleic acid subjected to fragmentation or cleavage mayhave a nominal, average or mean length of about 5 to about 10,000 basepairs, about 100 to about 1,000 base pairs, about 100 to about 500 basepairs, or about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,80, 85, 90, 95, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000,3000, 4000, 5000, 6000, 7000, 8000 or 9000 base pairs. Fragments can begenerated by a suitable method known in the art, and the average, meanor nominal length of nucleic acid fragments can be controlled byselecting an appropriate fragment-generating procedure. In certainembodiments, nucleic acid of a relatively shorter length can be utilizedto analyze sequences that contain little sequence variation and/orcontain relatively large amounts of known nucleotide sequenceinformation. In some embodiments, nucleic acid of a relatively longerlength can be utilized to analyze sequences that contain greatersequence variation and/or contain relatively small amounts of nucleotidesequence information.

Nucleic acid fragments may contain overlapping nucleotide sequences, andsuch overlapping sequences can facilitate construction of a nucleotidesequence of the non-fragmented counterpart nucleic acid, or a segmentthereof. For example, one fragment may have subsequences x and y andanother fragment may have subsequences y and z, where x, y and z arenucleotide sequences that can be 5 nucleotides in length or greater.Overlap sequence y can be utilized to facilitate construction of thex-y-z nucleotide sequence in nucleic acid from a sample in certainembodiments. Nucleic acid may be partially fragmented (e.g., from anincomplete or terminated specific cleavage reaction) or fully fragmentedin certain embodiments.

Nucleic acid can be fragmented by various methods known in the art,which include without limitation, physical, chemical and enzymaticprocesses. Non-limiting examples of such processes are described in U.S.Patent Application Publication No. 20050112590 (published on May 26,2005, entitled “Fragmentation-based methods and systems for sequencevariation detection and discovery,” naming Van Den Boom et al.). Certainprocesses can be selected to generate non-specifically cleaved fragmentsor specifically cleaved fragments. Non-limiting examples of processesthat can generate non-specifically cleaved fragment nucleic acidinclude, without limitation, contacting nucleic acid with apparatus thatexpose nucleic acid to shearing force (e.g., passing nucleic acidthrough a syringe needle; use of a French press); exposing nucleic acidto irradiation (e.g., gamma, x-ray, UV irradiation; fragment sizes canbe controlled by irradiation intensity); boiling nucleic acid in water(e.g., yields about 500 base pair fragments) and exposing nucleic acidto an acid and base hydrolysis process.

As used herein, “fragmentation” or “cleavage” refers to a procedure orconditions in which a nucleic acid molecule, such as a nucleic acidtemplate gene molecule or amplified product thereof, may be severed intotwo or more smaller nucleic acid molecules. Such fragmentation orcleavage can be sequence specific, base specific, or nonspecific, andcan be accomplished by any of a variety of methods, reagents orconditions, including, for example, chemical, enzymatic, physicalfragmentation.

As used herein, “fragments”, “cleavage products”, “cleaved products” orgrammatical variants thereof, refers to nucleic acid molecules resultantfrom a fragmentation or cleavage of a nucleic acid template genemolecule or amplified product thereof. While such fragments or cleavedproducts can refer to all nucleic acid molecules resultant from acleavage reaction, typically such fragments or cleaved products referonly to nucleic acid molecules resultant from a fragmentation orcleavage of a nucleic acid template gene molecule or the segment of anamplified product thereof containing the corresponding nucleotidesequence of a nucleic acid template gene molecule. For example, anamplified product can contain one or more nucleotides more than theamplified nucleotide region of a nucleic acid template sequence (e.g., aprimer can contain “extra” nucleotides such as a transcriptionalinitiation sequence, in addition to nucleotides complementary to anucleic acid template gene molecule, resulting in an amplified productcontaining “extra” nucleotides or nucleotides not corresponding to theamplified nucleotide region of the nucleic acid template gene molecule).Accordingly, fragments can include fragments arising from portions ofamplified nucleic acid molecules containing, at least in part,nucleotide sequence information from or based on the representativenucleic acid template molecule.

As used herein, the term “complementary cleavage reactions” refers tocleavage reactions that are carried out on the same nucleic acid usingdifferent cleavage reagents or by altering the cleavage specificity ofthe same cleavage reagent such that alternate cleavage patterns of thesame target or reference nucleic acid or protein are generated. Incertain embodiments, nucleic acid may be treated with one or morespecific cleavage agents (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or morespecific cleavage agents) in one or more reaction vessels (e.g., nucleicacid is treated with each specific cleavage agent in a separate vessel).

Nucleic acid may be specifically cleaved or non-specifically cleaved bycontacting the nucleic acid with one or more enzymatic cleavage agents(e.g., nucleases, restriction enzymes). The term “specific cleavageagent” as used herein refers to an agent, sometimes a chemical or anenzyme that can cleave a nucleic acid at one or more specific sites.Specific cleavage agents often cleave specifically according to aparticular nucleotide sequence at a particular site. Non-specificcleavage agents often cleave nucleic acids at non-specific sites ordegrade nucleic acids. Non-specific cleavage agents often degradenucleic acids by removal of nucleotides from the end (either the 5′ end,3′ end or both) of a nucleic acid strand.

Any suitable non-specific or specific enzymatic cleavage agent can beused to cleave or fragment nucleic acids. A suitable restriction enzymecan be used to cleave nucleic acids, in some embodiments. Examples ofenzymatic cleavage agents include without limitation endonucleases(e.g., DNase (e.g., DNase I, II); RNase (e.g., RNase E, F, H, P);Cleavase™ enzyme; Taq DNA polymerase; E. coli DNA polymerase I andeukaryotic structure-specific endonucleases; murine FEN-1 endonucleases;type I, II or III restriction endonucleases such as Acc I, Afl III, AluI, Alw44 I, Apa I, Asn I, Ava I, Ava II, BamH I, Ban II, Bcl I, Bgl I.Bgl II, Bln I, Bsm I, BssH II, BstE II, Cfo I, Cla I, Dde I, Dpn I, DraI, EclX I, EcoR I, EcoR I, EcoR II, EcoR V, Hae II, Hae II, Hind II,Hind III, Hpa I, Hpa II, Kpn I, Ksp I, Mlu I, MluN I, Msp I, Nci I, NcoI, Nde I, Nde II, Nhe I, Not I, Nru I, Nsi I, Pst I, Pvu I, Pvu II, RsaI, Sac I, Sal I, Sau3A I, Sca I, ScrF I, Sfi I, Sma I, Spe I, Sph I, SspI, Stu I, Sty I, Swa I, Taq I, Xba I, Xho I; glycosylases (e.g.,uracil-DNA glycosylase (UDG), 3-methyladenine DNA glycosylase,3-methyladenine DNA glycosylase II, pyrimidine hydrate-DNA glycosylase,FaPy-DNA glycosylase, thymine mismatch-DNA glycosylase, hypoxanthine-DNAglycosylase, 5-Hydroxymethyluracil DNA glycosylase (HmUDG),5-Hydroxymethylcytosine DNA glycosylase, or 1,N6-etheno-adenine DNAglycosylase); exonucleases (e.g., exonuclease III); ribozymes, andDNAzymes. Nucleic acid may be treated with a chemical agent, and themodified nucleic acid may be cleaved. In non-limiting examples, nucleicacid may be treated with (i) alkylating agents such as methylnitrosoureathat generate several alkylated bases, including N3-methyladenine andN3-methylguanine, which are recognized and cleaved by alkyl purineDNA-glycosylase; (ii) sodium bisulfite, which causes deamination ofcytosine residues in DNA to form uracil residues that can be cleaved byuracil N-glycosylase; and (iii) a chemical agent that converts guanineto its oxidized form, 8-hydroxyguanine, which can be cleaved byformamidopyrimidine DNA N-glycosylase. Examples of chemical cleavageprocesses include without limitation alkylation, (e.g., alkylation ofphosphorothioate-modified nucleic acid); cleavage of acid lability ofP3′-N5′-phosphoroamidate-containing nucleic acid; and osmium tetroxideand piperidine treatment of nucleic acid.

Nucleic acid also may be exposed to a process that modifies certainnucleotides in the nucleic acid before providing nucleic acid for amethod described herein. A process that selectively modifies nucleicacid based upon the methylation state of nucleotides therein can beapplied to nucleic acid, for example. In addition, conditions such ashigh temperature, ultraviolet radiation, x-radiation, can induce changesin the sequence of a nucleic acid molecule. Nucleic acid may be providedin any form useful for conducting a sequence analysis or manufactureprocess described herein, such as solid or liquid form, for example. Incertain embodiments, nucleic acid may be provided in a liquid formoptionally comprising one or more other components, including withoutlimitation one or more buffers or salts.

Nucleic acid may be single or double stranded. Single stranded DNA, forexample, can be generated by denaturing double stranded DNA by heatingor by treatment with alkali, for example. Nucleic acid sometimes is in aD-loop structure, formed by strand invasion of a duplex DNA molecule byan oligonucleotide or a DNA-like molecule such as peptide nucleic acid(PNA). D loop formation can be facilitated by addition of E. Coli RecAprotein and/or by alteration of salt concentration, for example, usingmethods known in the art.

Subpopulation Enrichment of Cell-Free Nucleic Acid

In some embodiments, the sample nucleic acid is processed such that asubpopulation of cell-free nucleic acid is enriched in the samplenucleic acid. In some embodiments, the enrichment is achieved byspecifically removing or depleting another subpopulation of cell-freenucleic acid. This method is sometimes referred to herein as “negativeenrichment”. Such negative enrichment methods can exploit differences incertain characteristics of nucleic acid subpopulations in a samplecomprising cell-free nucleic acid. For example, in some instances,cell-free nucleic acid is a mixture of vesicular and vesicle-freenucleic acid. By selectively depleting a sample nucleic acid ofvesicular nucleic acid, for example, the sample becomes enriched forvesicle-free nucleic acid, and vice-versa. In some instances, cell-freenucleic acid is a mixture of different vesicular nucleic acid species(e.g., vesicular nucleic acid having originated from different types oftissue). By selectively depleting a sample nucleic acid of a certainvesicular nucleic acid species, for example, the sample becomes enrichedfor a different vesicular nucleic acid species.

In some embodiments, the enrichment is achieved by specificallytargeting a desired subpopulation of cell-free nucleic acid. This methodis sometimes referred to herein as “positive enrichment”. Such positiveenrichment methods can exploit differences in certain characteristics ofnucleic acid subpopulations in a sample comprising cell-free nucleicacid. As mentioned above, in some instances, cell-free nucleic acid is amixture of different vesicular nucleic acid species (e.g., vesicularnucleic acid having originated from different types of tissue). Byselectively targeting a sample nucleic acid of a certain vesicularnucleic acid species, for example, the sample becomes enriched for suchvesicular nucleic acid species.

In another example, cell-free nucleic acid often is present innucleosome form. The particular histones and histone variants associatedwith such nucleosomal cell-free nucleic acid can vary depending on thecellular origin of the nucleic acid. Thus, certain subpopulations ofcell-free nucleic acid can be distinguished from one another based onthe type of histone and/or histone variant with which it is associated.By selectively depleting or targeting a sample nucleic acid of nucleicacid associated with one type of histone or histone variant, samplenucleic acid can become enriched for nucleic acid associated with adifferent histone or histone variant. Non-limiting examples of positiveand negative enrichment of cell-free nucleic acid are described infurther detail below.

Depletion of Vesicular Nucleic Acid

Cell-free nucleic acid often comprises a mixture of vesicular nucleicacid and vesicle-free nucleic acid. Vesicular nucleic acid is nucleicacid located in and/or associated with a vesicle or vesicle fragment. Asused herein, a vesicle is a small membrane-enclosed body that can storeor transport material. Often, the membrane enclosing the vesicle issimilar to that of the cellular plasma membrane and comprises at leastone phospholipid bilayer. Vesicles often are formed by a process inwhich a portion of a cellular membrane separates from the cell. Vesiclesmay also be referred to as microvesicles, nanovesicles, intralumenalvesicles, endosomal-like vesicles, exocytosed vesicles, microparticles,apoptotic bodies, apobodies, bleb, blebby, exosomes, dexosomes, andprostasomes. Vesicles sometimes are a byproduct of cell death (e.g.,apoptotic bodies, apobodies). Vesicles can include any shed membranebound particle that is derived from the plasma membrane or an internalmembrane. Vesicles also can include one or more cell-derived structuressurrounded by a lipid bilayer membrane. Vesicles also can includemembrane fragments.

Vesicles can be released into the extracellular environment from avariety of different cells such as but not limited to, endothelialcells, hemopoietic cells, and cells that have undergone genetic,environmental, and/or any other variations or alterations (e.g. tumorcells). Vesicles can have, for example, a diameter of less than 1micrometer. In some instances, vesicles can have a diameter that isabout 10 nanometers to about 600 nanometers. In some instances, vesiclescan have a diameter of about 40 nanometers to about 100 nanometers.Vesicles can have, for example, a diameter of about 45, 50, 55, 60, 65,70, 75, 80, 85, 90, or 95 nanometers. Certain vesicles can have adiameter of about 100 nanometers or greater. For example, certainvesicles can have a diameter of about 200 nanometers, 300 nanometers,400 nanometers, 500 nanometers, 600 nanometers, 700 nanometers, 800nanometers, 900 nanometers, 1000 nanometers, 1100 nanometers, 1200nanometers, 1300 nanometers, 1400 nanometers, 1500 nanometers orgreater.

The origins of vesicular nucleic acid and vesicle-free nucleic acid in acell-free nucleic acid sample can differ. For example, a cell freenucleic acid sample from a pregnant female can comprise vesicularnucleic acid of maternal and fetal origin and vesicle-free nucleic acidof maternal and fetal origin. The relative proportions of vesicular andvesicle-free nucleic acid can be different for maternal-derivedcell-free nucleic acid and fetal-derived cell-free nucleic acid. In someinstances, for example, the majority of maternal-derived cell-freenucleic acid can be vesicular and the majority of fetal-derivedcell-free nucleic acid can be vesicle-free. In another example,cell-free nucleic acid derived from tumors or solid organ transplantscan be substantially vesicle-free and cell-free nucleic acid derivedfrom normal or host tissue can be substantially vesicular. Without beinglimited by theory, such characteristics related to the presence orabsence of vesicular nucleic acid may account for size (i.e. nucleotidesequence length) differences observed for certain populations of cellfree nucleic acid. For example, cell-free DNA derived from fetal,transplant or tumor sources, can be enriched for a smaller subpopulationof DNA compared to cell-free DNA derived from, maternal, host or normalsources, respectively, as described, for example, in Chan et al. (2004)Clin Chem 50:88-92; Diehl et al. (2005) Proc Natl Acad Sci 102:16368-73;Lo et al. (2010) Sci Transl Med 2:61ra91; Zheng et al. (2011) Clin Chem169318; and Mouliere et al. (2011) PLoS One 6:9 e23418. In someinstances, for example, fetal cell-free DNA may include less of 166-bpsized DNA fragments and more of 143-bp sized DNA fragments compared tomaternal cell-free DNA. In some instances, the larger fragments may bepresent as vesicular DNA and thus may be less sensitive to circulatingnucleases, for example, and the smaller fragments may be present asvesicle-free DNA and thus more sensitive to circulating nucleases, forexample.

Vesicular nucleic acid and sometimes certain vesicular nucleic acidspecies (e.g., maternal derived vesicular nucleic acid) can be depletedfrom a sample using any method known in the art for separatingbiological material. Non-limiting separation methods include physicalseparation (e.g., filtration, centrifugation, dialysis, and the like)and methods that employ a binding agent. Filtration methods generallyinclude methods whereby the vesicular nucleic acid is absorbed by amembrane or barrier and the vesicle-free nucleic acid is retained in thesample. Various filtration methods are known in the art and include,without limitation, microfiltration, gel filtration, and magneticfiltration. Centrifugation methods generally include methods whereby aseparation of sample components is achieved by applying centrifugalforce. Various centrifugation methods are known in the art and include,without limitation, ultracentrifugation, differential centrifugation,equilibrium density-gradient centrifugation and zonal centrifugation.

Separation methods that employ a binding agent also can be used todeplete vesicular nucleic acid or a certain vesicular nucleic acidspecies in a sample. In such methods, components (i.e. vesicles) boundby the agent are separated away from the sample. A binding agent is anagent that specifically binds to a vesicle component, such as abiomarker. An agent “specifically binds” to a vesicle component if thebinding agent binds preferentially to the component, and, e.g., has lessthan about 30%, 20%, 10%, 5% or 1% cross-reactivity with anothermolecule. Methods for binding an agent to a vesicle are described, forexample, in US patent application publication nos. 2011/0151460,2010/0203529, and 2010/0184046. Binding agents can be monoclonalantibodies, polyclonal antibodies, Fabs, Fab′, single chain antibodies,synthetic antibodies, DNA, RNA, aptamers (DNA/RNA), peptoids, zDNA,peptide nucleic acids (PNAs), locked nucleic acids (LNAs), lectins,synthetic or naturally occurring chemical compounds (including but notlimited to drugs, labeling reagents), dendrimers, or combinationsthereof. For example, the binding agent can be a capture antibody. Suchbinding agents can be directly or indirectly coupled to a substrate orsolid support. Often, the substrate or solid support is used to separatethe vesicle from the sample. Some methods involve binding partners whereone partner is associated with the vesicle (e.g. conjugated to a vesiclebinding agent) and the other partner is associated with a solid support.In some instances, a single binding agent can be employed for thedepletion of vesicular nucleic acid. In some instances, a combination ofdifferent binding agents may be employed for the depletion of vesicularnucleic acid. For example, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 25, 50, 75 or 100 different bindingagents may be used to remove vesicular nucleic from a sample.

In some embodiments, a binding agent is specific for a componentassociated with a vesicle. Such components may include, for example,cell surface markers, membrane proteins, secreted factors or any othermolecule that can become associated with a vesicle. In some embodiments,the binding agent is specific for a component on the surface of avesicle. In some embodiments, the binding agent is specific for acomponent on a vesicle originating from a maternal cell. In someembodiments, the binding agent is specific for a component on a vesicleoriginating from a non-cancerous cell. In some embodiments, the bindingagent is specific for a component on a vesicle originating from a hostcell.

In some embodiments, the agent specifically binds to vesicles fromhemopoietic tissue. In some embodiments, the agent specifically binds tovesicles from red blood cells. In some embodiments, the agentspecifically binds to a vesicular component chosen from CD235a(glycophorin A), acetylcholinesterase, AMP deaminase, Band 3 (cdb3),BGP1, CD36, CD47, CD71 (transferrin receptor), chromium 51, erythrocytecreatine, globin, glycophorin B, hemoglobin, MBHb (membrane-boundhemoglobin), Rh Polypeptides, N-acetyl-9-O-acetylneuraminic acid,sequestrin, Ter119, thrombospondin (TSP), and VLA4. In some embodiments,the agent specifically binds to vesicles from leukocytes. In someembodiments, the agent specifically binds to a vesicular componentchosen from CD45, 8-OHdG (8-hydroxydeoxyguanosine), ATPase (adenosinetriphosphatase), beta2 leukocyte integrins (CD11/CD18), cathepsin G,CD15 (leuM1), CD18 (MHM23), CD43 (leukosialin, leu-22), CD53 (Ox-44),CD68 (KPI, macrosialin), CD95 (fas), CD166, diiodotyrosine (DIT), EFCC,fecal lactoferrin, glucose-6-phosphatase (G-6-Pase), HLA (humanleukocyte antigen), HLE (human leukocyte elastase), ICAM-1, IL-8(interleukin-8), L1, lactoferrin, LAM-1 (leukocyte adhesion molecule-1),LAP (leukocyte alkaline phosphatase), lectins, L-selectin, LSP1(leukocyte-specific protein-1), Ly-9, M6 (leukocyte activation antigen),Mac-1, MPO (myeloperoxidase), and VIP (vasoactive intestinalpolypeptide). In some embodiments, the agent specifically binds tovesicles from lymphocytes. In some embodiments, the agent specificallybinds to a vesicular component chosen from CD1a, CD1d, CD2, CD3, CD4,CD5, CD7, CD8, CD11b (Mac-1), CD16 (Leu 11b), CD19, CD20 (L26), CD21,CD22, CD24, CD25 (interleukin 2 receptor alpha), CD27, CD33, CD38, CD45,CD45RO, CD56, CD57, CD57/HNK1, CD69, CD72, CD79a, CD79b, CD86, CD90(Thy-1), CD107a, CD134 (OX40), CD150, CD161, CD244 (2B4), BAT, ART2,CRTAM, CS1, DPIV (dipeptidyl peptidase IV), GM-1, H25, H366, HNK-1 (Leu7), HP (helix pomatia) receptor, LAT (linker for activation of T cells),Ly24 (Pgp-1), NKH1 (N901), protocadherin 15 (PCDH15), sialyl SSEA-1,FOXP3, HLA-DR, HML-1, Leu-22, Ly-2, Ly-m22, MICG, MRC OX 8, MRC OX-22,PD-1, RT6, D8/17, FMC7, M17, MUM-1, Pax-5 (BSAP), PC47H, B220, BLAST-2(EBVCS), Bu-1, TSA-2 (thymic shared Ag-2), MHC class II, TCR alpha beta,and TCR gamma delta. In some embodiments, the agent specifically bindsto vesicles from granulocytes. In some embodiments, the agentspecifically binds to a vesicular component chosen from CD11b, CD15,CD16, CD18, CD24, CD32, CD34, CD45, CD66b, 3C4, 8C5, alkalinephosphatase, calprotectin, CEACAM8 (carcinoembryonic antigen-relatedcell adhesion molecule 8), DH59B, EMR3, eosinophil cationic protein(ECP), granulocyte factor (GF), GMP, Gr-1 (Ly-6G), granulocyte elastase,HIS48, interleukin-8 (IL-8), LAP (leukocyte alkaline phosphatase), LRG,Mac-1, myeloperoxidase (MPO), NKH1, Poly(ADP-ribose), VEP8, and VEP9. Insome embodiments, the agent specifically binds to vesicles frommonocytes. In some embodiments, the agent specifically binds to avesicular component chosen from CD11a (LFA-1 alpha), CD11b, CD14, CD15,CD54, CD62L (L-selectin), CD163, cytidine deaminase (CDD), Fc-receptors,125I-WVH-1, 63D3, adipophilin, angiotensin converting enzyme, CB12,FLT-1, HLA-DR, hMGL, Ki-M1p, leucocyte tartrate-resistant acidphosphatase (FATRE), Leu-7, lysozyme, mannosyl receptors, peanutagglutinin (PNA), thromboplastin, thymidine phosphorylase (TP), TNF(tumor necrosis factor), urokinase (UK), VEP8, and VEP9. In someembodiments, the agent specifically binds to vesicles from platelets. Insome embodiments, the agent specifically binds to a vesicular componentchosen from CD31, CD36, CD41, CD41a, CD42a, CD42b, CD49b, CD61, CD62,CD62P (P-selectin), CD63 (glycoprotein-53), AK (adenylate kinase),annexin V, BTG (beta-thromboglobulin), glycocalicin (GC), GMP-140(platelet alpha-granule membrane protein), GPV (glycoprotein V),imidazoline receptors (IR-1), LAMP2 (lysosome-associated membraneprotein-2), PAC-1, PDMP (platelet-derived microparticles),platelet-associated factor XIIIa, platelet factor 4 (PF4), S12,serotonin (5-HT), thrombospondin (TSP), and thromboxane B2.

In some embodiments, the agent specifically binds to vesicles fromendothelial cells. In some embodiments, the agent specifically binds toa vesicular component chosen from CD31 (PECAM-1), CD34, CD54 (ICAM-1),CD62E, CD62P (p-Selectin GMP140), CD51, CD105 (Endoglin), CD106 (VCAM-1,vascular cell adhesion molecule-1), CD144 (VE-cadherin), CD146 (P1H12),7B4 antigen, ACE (angiotensin-converting enzyme), BNH9/BNF13, D2-40,E-selectin, EN4, Endocan (ESM-1), Endoglyx-1, Endomuci, Endosialin(TEM-1, FB5), Eotaxin-3, EPAS1, Factor VIII related antigen, FB21, Flk-1(VEGFR-2), Flt-1 (VEGFR-1), GBP-1 (guanylate-binding protein-1),GRO-alpha, Hex, ICAM-2 (intercellular adhesion molecule 2), LYVE-1,MECA-32, MECA-79, MRB (magic roundabout), Nucleolin, PALE (pathologischeanatomie Leiden-endothelium), RPTPmu (receptor protein tyrosinephosphatase mu), RTKs, TEM1 (Tumor endothelial marker 1), TEM5 (Tumorendothelial marker 5), TEM7 (Tumor endothelial marker 7), TEM8 (Tumorendothelial marker 8), Thrombomodulin (TM, CD141), VEGF (vascularendothelial growth factor), and vWF (von Willebrand factor).

In some embodiments, the binding agent is an antibody. For example, avesicle (e.g., a vesicle comprising nucleic acid) may be removed from asample using one or more antibodies specific for one or more antigenspresent on the vesicle. Antibodies can be immunoglobulin molecules orimmunologically active portions of immunoglobulin molecules, i.e.,molecules that contain an antigen binding site that specifically bindsan antigen. A variety of antibodies and antibody fragments are availableto and can be generated by the artisan for use as a specific bindingagent. Antibodies sometimes are IgG, IgM, IgA, IgE, or an isotypethereof (e.g., IgG1, IgG2a, IgG2b or IgG3), sometimes are polyclonal ormonoclonal, and sometimes are chimeric, humanized or bispecific versionsof such antibodies. Polyclonal and monoclonal antibodies that bindspecific antigens are commercially available, and methods for generatingsuch antibodies are known. The binding agent also can be a polypeptideor peptide. The term polypeptide is used herein in its broadest senseand may include a sequence of amino acids, amino acid analogs, orpeptidomimetics, typically linked by peptide bonds. The polypeptides maybe naturally occurring, processed forms of naturally occurringpolypeptides (such as by enzymatic digestion), chemically synthesized,or recombinantly expressed. The polypeptides for use in the methodsherein may be chemically synthesized using standard techniques. Thepolypeptides may comprise D-amino acids (which are resistant to L-aminoacid-specific proteases), a combination of D- and L-amino acids, betaamino acids, or various other designer or non-naturally occurring aminoacids (e.g., beta-methyl amino acids, C alpha-methyl amino acids, Nalpha-methyl amino acids, and the like) to convey special properties.Synthetic amino acids may include ornithine for lysine, and norleucinefor leucine or isoleucine. In some instances, polypeptides can havepeptidomimetic bonds, such as ester bonds, to prepare polypeptides withnovel properties. Polypeptides can also include peptoids (N-substitutedglycines), in which the side chains are appended to nitrogen atoms alongthe molecule's backbone, rather than to the alpha-carbons, as in aminoacids.

In some embodiments, a binding agent can be linked directly orindirectly to a solid support or substrate. In some embodiments,vesicles are associated with a solid support, such as the solid supportsdescribed below, by one or more binding agents, such as the bindingagents described herein. A solid support or substrate can be anyphysically separable solid to which a binding agent can be directly orindirectly attached including, but not limited to, surfaces provided bymicroarrays and wells, and particles such as beads (e.g., paramagneticbeads, magnetic beads, microbeads, nanobeads), microparticles, andnanoparticles. Solid supports also can include, for example, chips,columns, optical fibers, wipes, filters (e.g., flat surface filters),one or more capillaries, glass and modified or functionalized glass(e.g., controlled-pore glass (CPG)), quartz, mica, diazotized membranes(paper or nylon), polyformaldehyde, cellulose, cellulose acetate, paper,ceramics, metals, metalloids, semiconductive materials, quantum dots,coated beads or particles, other chromatographic materials, magneticparticles; plastics (including acrylics, polystyrene, copolymers ofstyrene or other materials, polybutylene, polyurethanes, TEFLON™,polyethylene, polypropylene, polyamide, polyester,polyvinylidenedifluoride (PVDF), and the like), polysaccharides, nylonor nitrocellulose, resins, silica or silica-based materials includingsilicon, silica gel, and modified silicon, Sephadex®, Sepharose®,carbon, metals (e.g., steel, gold, silver, aluminum, silicon andcopper), inorganic glasses, conducting polymers (including polymers suchas polypyrole and polyindole); micro or nanostructured surfaces such asnucleic acid tiling arrays, nanotube, nanowire, or nanoparticulatedecorated surfaces; or porous surfaces or gels such as methacrylates,acrylamides, sugar polymers, cellulose, silicates, or other fibrous orstranded polymers. In some instances, the solid support or substrate maybe coated using passive or chemically-derivatized coatings with anynumber of materials, including polymers, such as dextrans, acrylamides,gelatins or agarose. Beads and/or particles may be free or in connectionwith one another (e.g., sintered). In some embodiments, the solid phasecan be a collection of particles. In certain embodiments, the particlescan comprise silica, and the silica may comprise silica dioxide. In someembodiments the silica can be porous, and in certain embodiments thesilica can be non-porous. In some embodiments, the particles furthercomprise an agent that confers a paramagnetic property to the particles.In certain embodiments, the agent comprises a metal, and in certainembodiments the agent is a metal oxide, (e.g., iron or iron oxides,where the iron oxide contains a mixture of Fe2+ and Fe3+).

Using the methods described herein, vesicles (and the nucleic acidtherein) can be separated away from a sample nucleic acid, therebygenerating a separation product. Separation products can be partially orsubstantially free of vesicular nucleic acid. As used herein, the term“partially or substantially free” refers to a separation product forwhich at least about 50% to about 100% of the vesicular nucleic acid hasbeen depleted. For example, a separation product that is partially orsubstantially free of vesicular nucleic acid has had at least about 60%,70%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or 99.9% of vesicular nucleicacid depleted. In certain embodiments, separation products can bepartially or substantially free of vesicular nucleic acid originatingfrom maternal cells. In certain embodiments, separation products can bepartially or substantially free of vesicular nucleic acid originatingfrom host cells. In certain embodiments, separation products can bepartially or substantially free of vesicular nucleic acid originatingfrom non-cancerous cells. In certain embodiments, separation productscan be partially or substantially free of vesicular nucleic acidoriginating from endothelial cells. In certain embodiments, separationproducts can be partially or substantially free of vesicular nucleicacid originating from hematopoietic cells. In certain embodiments,separation products can be partially or substantially free of vesicularnucleic acid originating from red blood cells. In certain embodiments,separation products can be partially or substantially free of vesicularnucleic acid originating from leukocytes. In certain embodiments,separation products can be partially or substantially free of vesicularnucleic acid originating from lymphocytes. In certain embodiments,separation products can be partially or substantially free of vesicularnucleic acid originating from granulocytes. In certain embodiments,separation products can be partially or substantially free of vesicularnucleic acid originating from monocytes. In certain embodiments,separation products can be partially or substantially free of vesicularnucleic acid originating from platelets.

Selection of Vesicular Nucleic Acid

In some embodiments, a vesicular nucleic acid species is enriched usinga positive enrichment approach. For example, in some embodiments, afetal-derived vesicular nucleic acid species is enriched by selectivelytargeting a specific feature (e.g., biomarker) of the fetal derivedvesicle, as described above. In some embodiments a fetal-derived vesicleis an apoptotic body. In some embodiments, a fetal-derived vesicularnucleic acid species is enriched using a centrifugation method.Centrifugation methods generally include methods whereby a separation ofsample components is achieved by applying centrifugal force. Variouscentrifugation methods are known in the art and include, withoutlimitation, ultracentrifugation, differential centrifugation,equilibrium density-gradient centrifugation and zonal centrifugation.

In some instances, centrifugation can separate components of a sample(e.g., microparticles, apoptotic bodies) and thus enrich for asubpopulation of nucleic acid associated with such components. Thus,without being limited by theory, if a larger proportion of fetal nucleicacid is associated with a certain sample component (e.g., apoptoticbodies) than maternal nucleic acid, then enrichment of the samplecomponent using centrifugation can enrich for fetal nucleic acid. Insome instances, without being limited by theory, if a larger proportionof maternal nucleic acid is associated with a certain sample component(e.g., apoptotic bodies) than fetal nucleic acid, then depletion of thesample component using centrifugation can enrich for fetal nucleic acid.In some embodiments, centrifugation comprises use of ultracentrifugation(e.g., high speed centrifugation). A centrifugation process typicallygenerates a supernatant and a pellet, or zones within a gradient (e.g.,density gradient), in certain instances. In some embodiments, fetalnucleic acid is enriched in the supernatant. In some embodiments, fetalnucleic acid is enriched in the pellet. In some embodiments, fetalnucleic acid is enriched in one or more zones within a gradient. In someembodiments, the supernatant is subjected to one or more furthercentrifugations. In some embodiments, the pellet is subjected to one ormore further centrifugations.

To achieve a desired separation of sample components, one or more ofspeed, duration and amount of centrifugation can be adjusted. In someembodiments, a centrifugation speed of about 1000 g or greater is used.For example, a centrifugation speed of about 1200 g, 1300 g, 1400 g,1500 g, 1600 g, 1800 g, 2000 g, 2200 g, 2400 g, 2500 g, 2600 g, 2800 g,or 3000 g or greater can be used. In some embodiments, a centrifugationspeed of about 1600 g is used. In some embodiments, a centrifugationspeed of about 2500 g is used. In some embodiments, a centrifugationspeed of about 20,000 g or greater is used. For example, acentrifugation speed of about 21,000 g, 22,000 g, 23,000 g, 24,000 g,25,000 g, 26,000 g, 27,000 g, 28,000 g, 29,000 g, or 30,000 g or greatercan be used. In some embodiments, a centrifugation speed of about 25,000g is used. In some embodiments, a centrifugation speed of about 80,000 gor greater is used. For example, a centrifugation speed of about 80,000g, 90,000 g, 95,000 g, 96,000 g, 97,000 g, 98,000 g, 99,000 g, 100,000g, 101,000 g, 102,000 g, 103,000 g, 104,000 g, 105,000 g, 110,000 g orgreater can be used. In some embodiments, a speed of about 100,000 g isused.

In some embodiments, a centrifugation duration of about 1 minute orgreater is used. For example, a centrifugation duration of about 5minutes, 10 minutes, 15 minutes, 20 minutes, 30 minutes, 40 minutes, 50minutes, 60 minutes, 90 minutes, or 120 minutes or greater can be used.In some embodiments, a centrifugation duration of about 10 minutes isused. In some embodiments, a centrifugation duration of about 15 minutesis used. In some embodiments, a centrifugation duration of about 60minutes is used.

Depletion of a Histone-Associated Nucleic Acid Species

Provided herein are methods for enriching a subpopulation of cell-freenucleic acid in a sample by separating a different subpopulation ofcell-free nucleic acid associated with a certain histone or histonevariant away from the sample. Histones are nuclear proteins that make upthe nucleosome structure of the chromosomal fiber in eukaryotes.Nucleosomes generally comprise approximately 146 base pairs of DNAwrapped around a histone octamer which includes pairs of each of thefour core histones (H2A, H2B, H3, and H4). The chromatin fiber can befurther compacted through the interaction of a linker histone, H1, withthe DNA between the nucleosomes to form higher order chromatinstructures. Methylation of position-specific lysine residues in histoneN termini can help regulate epigenetic transitions in chromatin. Certainlysine residues can exist in a mono-, di-, or trimethylated state.Arginine residues can also be mono- or dimethylated.

As used herein, “histone variant” refers to various post-translationalhistone modifications (e.g., methylation, acetylation, phosphorylationand the like) and histone isoforms, epitopes or subtypes. For example,the H3 class of histones includes of four different sub-types: the maintypes, H3.1 and H3.2; the replacement type, H3.3; and the testisspecific variant, H3t. H3.1 and H3.2 are closely related, only differingat Ser96. H3.1 differs from H3.3 in at least 5 amino acid positions. Inanother example, the linker histone H1 includes several subtypesincluding H1a, H1b, H1c, H1d, H1e, H1m, and H1(0), each of whichcomprises various amino acid sequence differences.

Differences in histones and/or histone variants can be exploited for theseparation of certain subpopulations of cell-free nucleic acid away froma sample, thereby enriching for another subpopulation of cell-freenucleic acid. For example, a cell-free circulating sample nucleic acidfrom a biological sample can comprise a first histone-associated nucleicacid species and a second histone-associated nucleic acid species. Someor substantially all of the first histone-associated nucleic acidspecies can be separated from the sample nucleic acid, therebygenerating a separation product enriched for the secondhistone-associated nucleic acid species.

Differences in histones and/or histone variants also can be exploitedfor the enrichment of fetal nucleic acid in sample nucleic acid thatincludes fetal nucleic acid and maternal nucleic acid. In someinstances, cell-free circulating sample nucleic acid from a biologicalsample from a pregnant female comprises a first histone-associatednucleic acid species and a second histone-associated nucleic acidspecies. Some or substantially all of the first histone-associatednucleic acid species can be separated from the sample nucleic acid,thereby generating a separation product enriched for the secondhistone-associated nucleic acid species, where fetal nucleic acid in theseparation product is enriched relative to fetal nucleic acid in thesample nucleic acid.

In one example, histone H3.1 can be highly enriched in fetal liver,compared to histone H3.1 levels in adult tissues including liver, kidneyand heart. In adult tissue, the H3.3 variant can be more abundant thanthe H3.1 variant (see e.g., United States Patent Application Publicationnos. 2007/0243549 and 2010/0240054). Thus, a first histone-associatednucleic acid species can be a nucleic acid associated with histone H3.3and a second histone-associated nucleic acid species can be a nucleicacid associated with histone H3.1. Because histone H3.1 can be enrichedin fetal tissue, separating some or substantially all of the firsthistone-associated nucleic acid species (i.e. histone H3.3 associatednucleic acid) from the sample nucleic acid can deplete a proportion ofmaternal nucleic acid and generate a separation product enriched forfetal nucleic acid relative to fetal nucleic acid in the sample nucleicacid. In some instances, the conformational structure of fetal DNA innucleosomes is such that histone H3.1 is more exposed in fetal DNA thanin maternal DNA. Such a difference can also be exploited to targethistone H3.1.

In another example, histone H1a can be enriched in fetal retina,compared to histone H1a levels in adult retina, which can haverelatively higher levels of histone H1b and H1(0) (see Perkins and Young(1987) Jpn J Ophthalmol. 31(4):590-7). Thus, a first histone-associatednucleic acid species can be a nucleic acid associated with histone H1band/or H1(0) and a second histone-associated nucleic acid species can bea nucleic acid associated with histone H1a. Because histone H1a can beenriched in certain fetal tissue, separating some or substantially allof the first histone-associated nucleic acid species (i.e. histone H1band/or H1(0) associated nucleic acid) from the sample nucleic acid candeplete a proportion of maternal nucleic acid and generate a separationproduct enriched for fetal nucleic acid relative to fetal nucleic acidin the sample nucleic acid.

In another example, certain subpopulations of cell-free nucleic acid canbe associated with histones comprising one or more posttranslationalmodifications such as methylation, acetylation, phosphorylation, and thelike. For instance, fetal nucleic acid may be associated with amethylated histone, such as, for example a methylated histone H1 or H3(e.g., H3.1), and maternal nucleic acid may be associated with anunmethylated histone, such as, for example an unmethylated histone H1 orH3 (e.g., H3.1). Thus, a first histone-associated nucleic acid speciescan be a nucleic acid associated with an unmodified histone and a secondhistone-associated nucleic acid species can be a nucleic acid associatedwith a posttranslationally modified histone. Because fetal tissue can beenriched for histones comprising certain posttranslationalmodifications, separating some or substantially all of the firsthistone-associated nucleic acid species (i.e. nucleic acid associatedwith an unmodified histone) from the sample nucleic acid can deplete aproportion of maternal nucleic acid and generate a separation productenriched for fetal nucleic acid relative to fetal nucleic acid in thesample nucleic acid.

Separation methods that employ a binding agent, for example, can be usedto deplete a particular histone-associated nucleic acid in a sample. Insuch methods, histone proteins (and the histone-associated nucleic acid)bound by the agent are separated away from the sample. A binding agentis an agent that specifically binds to a particular histone or histonevariant. An agent “specifically binds” to a histone or histone variantif the binding agent binds preferentially to the histone or histonevariant and, e.g., has less than about 30%, 20%, 10%, 5% or 1%cross-reactivity with another molecule. Methods for binding an agent toa histone or histone variant are described, for example, in US patentapplication publication nos. 2007/0243549 and 2010/0240054. Bindingagents can be any binding agent known in the art or described herein,such as antibodies as described above. In some embodiments, the bindingagent (e.g., antibody) is coupled to a solid support as described above.Such separation methods may include a lysis step to release nucleic acidcontained in vesicles, in some embodiments. Methods for lysing vesiclesare known in the art and generally include the use of a commerciallyavailable lysis buffer.

In some embodiments, the binding agent is specific for a particularhistone or histone variant. Such histones or histone variants mayinclude, for example, any histone protein, subtype, epitope, or isoformdescribed herein or known in the art, each of which may include any ofthe posttranslational modifications described herein or known in the artor which may be unmodified. In some embodiments, the binding agent isspecific for a histone originating from a maternal cell. In someembodiments, the binding agent is specific for a modified histone. Insome embodiments, the binding agent is specific for a modified histonecomprising a certain amount and/or combination of posttranslationalmodifications, such as, for example methylation, phosphorylation and/oracetylation. In some embodiments, the binding agent is specific for amethylated histone. In some embodiments, the binding agent is specificfor an acetylated histone. In some embodiments, the binding agent isspecific for a phosphorylated histone. In some embodiments, the bindingagent is specific for an unmodified histone. In some embodiments, thebinding agent is specific for an unmethylated histone. In someembodiments, the binding agent is specific for a non-acetylated histone.In some embodiments, the binding agent is specific for anon-phosphorylated histone. In some embodiments, the binding agent isspecific for histone H3.3. In some embodiments, the binding agent isspecific for histone H1b and/or H1(0).

In some embodiments, a sample can be enriched for a subpopulation ofcell-free nucleic acid by the depletion of nucleic acid associated witha particular histone or histone variant. For example, a cell-freecirculating sample nucleic acid from a biological sample can comprise afirst histone-associated nucleic acid species and a secondhistone-associated nucleic acid species. Some or substantially all ofthe first histone-associated nucleic acid species can be separated fromthe sample nucleic acid, thereby generating a separation productenriched for the second histone-associated nucleic acid species. In someembodiments, the separation product comprises about 50% or greater of asecond histone-associated nucleic acid species. For example, theseparation product can comprise about 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95% or 100% of a second histone-associated nucleic acid species. Insome embodiments, fetal nucleic acid in the separation product isenriched relative to fetal nucleic acid in the sample nucleic acid. Insome embodiments, fetal nucleic acid in the separation product can beenriched about 1.5-fold to about 20-fold relative to fetal nucleic acidin the sample nucleic acid. For example, fetal nucleic acid can beenriched about 2, 3, 4, 5, 6, 7, 8, 9, 10, or 15-fold.

Separation of Histone Associated Nucleic Acid Species

In some embodiments, a method comprises separating some or substantiallyall of a first histone-associated nucleic acid species from a secondhistone-associated nucleic acid species, thereby generating a separationproduct enriched for the second histone-associated nucleic acid species.In some embodiments, fetal nucleic acid in the separation product isenriched relative to fetal nucleic acid in the sample nucleic acid. Incertain instances, circulating cell free fetal DNA can be associatedwith microparticles and nucleosomes (e.g., histone bound) that arederived from fetal tissue. In certain instances, circulating cell freematernal DNA can be associated with microparticles and nucleosomes(e.g., histone bound) that are derived from maternal tissue. Thus, insome embodiments, utilization of fetal source-specific binding agents(e.g., antibodies) to target fetal-derived microparticles and/ornucleosomes can enrich fetal DNA. In some embodiments, utilization ofmaternal source-specific binding agents (e.g., antibodies) to targetmaternal-derived microparticles and/or nucleosomes can enrich fetal DNA.

Nucleosome DNA typically is associated with an octamer of eight corehistones: H2A (2), H2B (2), H3 (2), and H4 (2); and a linker histone H1.In maternal blood and cleared plasma, fetal ccf DNA may have a loweroccupancy of H1 (i.e., a smaller percentage of the nucleosome DNA offetal origin may have H1 bound, relative to the percentage of maternalccf DNA having H1 bound). Without being limited by theory, the typicalsize distribution of fetal ccf DNA versus maternal ccf DNA is inaccordance with this concept, since nucleosome DNA without H1 bound maybe more susceptible to endonuclease digestion, thus resulting in shorterfragments.

In some embodiments, an agent that binds to histone H1 (e.g., withoutparticular specificity to H1 subtypes or sources) is used as a tool fora negative selection approach to enrich for fetal DNA. Treatment ofplasma with such an agent (e.g., antibody), for example, in animmunoprecipitation (e.g., Chromatin ImmunoPrecipitation (CHIP))protocol can deplete maternal ccf DNA from the sample, thus enhancingccf DNA fetal fraction in the residual sample.

In some embodiments, antibodies to fetal-specific histones (e.g., H1.1,H1.3, H1.5), are used to enrich fetal ccf DNA in certain positiveselection approaches. In some embodiments, antibodies tomaternal-specific histones (e.g., H1, H1.0), are used to enrich fetalccf DNA in certain depletion-based entichment (i.e., negative selection)approaches. In some embodiments, antibodies to H1M histone (expressed inXenopus embryos) and/or to H1FOO (which are expressed in oocytes) areused to enrich fetal ccf DNA in certain positive selection approaches.These approaches can include any suitable separation method describedherein or known in the art such as conventional immunoprecipitation andChromatin ImmunoPrecipitation (CHIP) approaches, for example.

There are approximately eleven H1 variants, some of which may bespecific (or show preferential binding) to fetal-derived ccf DNA.Additionally, various maternal versus fetal differences in H3 histonesubtype can be exploited to enrich for fetal fraction. For example,antibodies recognizing conformational exposure differences for histoneH3.1 (e.g., differences between fetal and maternal H3.1) can be used forfetal DNA enrichment from plasma treated with such antibodies, incertain embodiments. For example, sequence variance (e.g., extra 10amino acids at the c-terminus of fetal H3.1), and particular methylationof H3.1 in fetal versus maternal can be exploited for fetal DNAenrichment, in certain embodiments.

Methods for identifying certain antibodies (e.g., selective forfetal-derived histones and/or nucleosomes versus maternal-derivedhistones and/or nucleosomes) from commercial or elicited populations ofantibodies, antibody fragments or aptamers are described in Example 1.

Enrichment of a Nucleic Acid Sub-Population

Methods provided herein can generate separation products that areenriched for a subpopulation of nucleic acid (e.g., enriched for asub-population of cell-free nucleic acid). In certain embodiments,separation products can be enriched for vesicle-free nucleic acid bydepletion vesicular nucleic acid. In some embodiments, a separationproduct comprises about 50% or greater vesicle-free nucleic acid. Forexample, a separation product can comprise about 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, 95% or 100% vesicle-free nucleic acid. In someembodiments, some or substantially all vesicular nucleic acid isseparated from sample nucleic acid, thereby generating a separationproduct enriched for vesicle-free nucleic acid.

In certain embodiments, a separation product can be enriched forhistone-free nucleic acid by depletion of histone-associated nucleicacid. In some embodiments, a separation product comprises about 50% orgreater histone-free nucleic acid. For example, a separation product cancomprise about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100%histone-free nucleic acid. In some embodiments, some or substantiallyall histone-associated nucleic acid is separated from sample nucleicacid, thereby generating a separation product enriched for histone-freenucleic acid.

In some embodiments, a separation product is enriched for nucleic acidassociated with a particular histone species or group of histonespecies. Nucleic acid associated with a particular histone species orgroup of histone species can be separated from histones, andconsequently, a separation product sometimes is enriched for nucleicacid that was associated with a particular histone species or group ofhistone species. In certain embodiments, a separation product can beenriched for histone-associated nucleic acid by contacting samplenucleic acid with a binding agent that specifically binds to aparticular histone species or group of histone species and separatingnucleic acid associated with the agent (e.g., nucleic acid bound to theagent, or nucleic acid in a complex bound to the agent) from nucleicacid not bound to the agent. In some embodiments, a separation productcomprises about 50% or greater histone-associated nucleic acid, or about50% or greater nucleic acid that was in association with a particularhistone species or group of histone species. For example, a separationproduct can comprise about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%or 100% histone-associated nucleic acid or nucleic acid that was inassociation with a particular histone species or group of histonespecies. In some embodiments, some or substantially all of nucleic acidnot associated with a particular histone species or group of histonespecies is separated from nucleic acid associated with, or wasassociated with, the particular histone species or group of histonespecies, thereby generating a separation product enriched for thehistone-associated nucleic acid, or nucleic acid that was associatedwith the histone or group of histones.

In some embodiments, fetal nucleic acid in a separation product isenriched relative to fetal nucleic acid in sample nucleic acid. Incertain embodiments, the relative proportion of (i) fetal nucleic acidto (ii) non-fetal nucleic acid is greater in the separation product thanin the sample nucleic acid. For determining such a proportion, non-fetalnucleic acid sometimes is maternal nucleic acid, totalhistone-associated nucleic acid, total vesicle-associated nucleic acidor total nucleic acid (e.g., histone-associated nucleic acid andnon-histone-associated nucleic acid; vesicle-associated nucleic acid andnon-vesicle-associated nucleic acid). Fetal nucleic acid in a separationproduct sometimes is enriched 1.5-fold to 1,000-fold relative to fetalnucleic acid in sample nucleic acid (e.g., 20, 30, 40, 50, 60, 70, 80,90, 100, 200, 300, 400, 500, 600, 700, 800 or 900-fold enriched). Insome embodiments, fetal nucleic acid in the separation product can beenriched about 1.5-fold to about 20-fold relative to fetal nucleic acidin sample nucleic acid. For example, fetal nucleic acid can be enrichedabout 2, 3, 4, 5, 6, 7, 8, 9, 10, or 15-fold. In some embodiments,tumor-derived nucleic acid in a separation product is enriched relativeto tumor-derived nucleic acid in sample nucleic acid. In someembodiments, nucleic acid derived from solid organ transplants in aseparation product is enriched relative to nucleic acid derived fromsolid organ transplants in the sample nucleic acid.

In some embodiments, a nucleic acid sample can be further enriched for aparticular subpopulation of cell-free nucleic acid by a method known inthe art or described herein. For example, a nucleic acid sample can befurther enriched for a particular subpopulation of cell-free nucleicacid by contacting nucleic acid that is substantially vesicle free withan agent that specifically binds to a histone associated with thevesicle-free nucleic acid. In certain embodiments, the histone isassociated with a subpopulation of cell-free nucleic acid that isdifferent from the enriched subpopulation of cell-free nucleic acid. Forexample, the histone can be associated with maternal cell-free nucleicacid. Methods for enriching a subpopulation of cell-free nucleic acidusing histone binding agents are described in further detail herein.

A separation product containing fetal nucleic acid often contains fetalnucleic acid fragments. Fetal nucleic acid fragments in a separationproduct often range in size from about 50 base pairs to about 200 basepairs. The entire fetal genome or significant fraction of the fetalgenome (e.g., 70% or more of the fetal genome) sometimes is representedin a separation product. Fetal nucleic acid fragments having the samelength (e.g., 149 base pair fragment length or 150 base pair fragmentlength) in a separation product often represent a large number ofsequences. There often are many fetal nucleic acid fragments having thesame length but different sequences in a separation product. In someembodiments, about 1/15th of the fetal genome is represented by fetalnucleic acid fragments having the same length (e.g., 1/12th to 1/18th(e.g., 1/13th, 1/14th, 1/16th, 1/17th, 1/18th)). Fetal nucleic acidfragments having a particular length in a separation product often arefrom multiple and distinct regions of the genome. Some or all fetalnucleic acid fragments in a separation product often have sizesseparated by one base pair (1-bp), where each fragment is 1-bp largerthan the next shorter fragment.

Further Enrichment of Cell-Free Nucleic Acid

In some embodiments, nucleic acid (e.g., extracellular nucleic acid) isenriched or relatively enriched for a subpopulation or species ofnucleic acid using a method described herein and one or more additionalenrichment methods. Nucleic acid subpopulations can include, forexample, fetal nucleic acid, maternal nucleic acid, nucleic acidcomprising fragments of a particular length or range of lengths, ornucleic acid from a particular genome region (e.g., single chromosome,set of chromosomes, and/or certain chromosome regions). Such enrichedsamples can be used in conjunction with a method provided herein. Thus,in certain embodiments, methods of the technology comprise an additionalstep of enriching for a subpopulation of nucleic acid in a sample, suchas, for example, fetal nucleic acid. In some embodiments, certainmethods for determining fetal fraction described below also can be usedto enrich for fetal nucleic acid. In certain embodiments, maternalnucleic acid is selectively removed (partially, substantially, almostcompletely or completely) from the sample. In some embodiments,enriching for a particular low copy number species nucleic acid (e.g.,fetal nucleic acid) may improve quantitative sensitivity. Methods forenriching a sample for a particular species of nucleic acid aredescribed, for example, in U.S. Pat. No. 6,927,028, International PatentApplication Publication No. WO2007/140417, International PatentApplication Publication No. WO2007/147063, International PatentApplication Publication No. WO2009/032779, International PatentApplication Publication No. WO2009/032781, International PatentApplication Publication No. WO2010/033639, International PatentApplication Publication No. WO2011/034631, International PatentApplication Publication No. WO2006/056480, and International PatentApplication Publication No. WO2011/143659, all of which are incorporatedby reference herein.

In some embodiments, nucleic acid is enriched for certain targetfragment species and/or reference fragment species. In some embodiments,nucleic acid is enriched for a specific nucleic acid fragment length orrange of fragment lengths using one or more length-based separationmethods described below. In some embodiments, nucleic acid is enrichedfor fragments from a select genomic region (e.g., chromosome) using oneor more sequence-based separation methods described herein and/or knownin the art. Certain methods for enriching for a nucleic acidsubpopulation (e.g., fetal nucleic acid) in a sample are described indetail below.

Some methods for enriching for a nucleic acid subpopulation (e.g., fetalnucleic acid) that can be used with a method described herein includemethods that exploit epigenetic differences between maternal and fetalnucleic acid. For example, fetal nucleic acid can be differentiated andseparated from maternal nucleic acid based on methylation differences.Methylation-based fetal nucleic acid enrichment methods are described inU.S. Patent Application Publication No. 2010/0105049, which isincorporated by reference herein. Such methods sometimes involve bindinga sample nucleic acid to a methylation-specific binding agent(methyl-CpG binding protein (MBD), methylation specific antibodies, andthe like) and separating bound nucleic acid from unbound nucleic acidbased on differential methylation status. Such methods also can includethe use of methylation-sensitive restriction enzymes (as describedabove; e.g., HhaI and HpaII), which allow for the enrichment of fetalnucleic acid regions in a maternal sample by selectively digestingnucleic acid from the maternal sample with an enzyme that selectivelyand completely or substantially digests the maternal nucleic acid toenrich the sample for at least one fetal nucleic acid region.

Another method for enriching for a nucleic acid subpopulation (e.g.,fetal nucleic acid) that can be used with a method described herein is arestriction endonuclease enhanced polymorphic sequence approach, such asa method described in U.S. Patent Application Publication No.2009/0317818, which is incorporated by reference herein. Such methodsinclude cleavage of nucleic acid comprising a non-target allele with arestriction endonuclease that recognizes the nucleic acid comprising thenon-target allele but not the target allele; and amplification ofuncleaved nucleic acid but not cleaved nucleic acid, where theuncleaved, amplified nucleic acid represents enriched target nucleicacid (e.g., fetal nucleic acid) relative to non-target nucleic acid(e.g., maternal nucleic acid). In some embodiments, nucleic acid may beselected such that it comprises an allele having a polymorphic site thatis susceptible to selective digestion by a cleavage agent, for example.

Some methods for enriching for a nucleic acid subpopulation (e.g., fetalnucleic acid) that can be used with a method described herein includeselective enzymatic degradation approaches. Such methods involveprotecting target sequences from exonuclease digestion therebyfacilitating the elimination in a sample of undesired sequences (e.g.,maternal DNA). For example, in one approach, sample nucleic acid isdenatured to generate single stranded nucleic acid, single strandednucleic acid is contacted with at least one target-specific primer pairunder suitable annealing conditions, annealed primers are extended bynucleotide polymerization generating double stranded target sequences,and digesting single stranded nucleic acid using a nuclease that digestssingle stranded (i.e., non-target) nucleic acid. In some embodiments,the method can be repeated for at least one additional cycle. In someembodiments, the same target-specific primer pair is used to prime eachof the first and second cycles of extension, and in some embodiments,different target-specific primer pairs are used for the first and secondcycles.

Some methods for enriching for a nucleic acid subpopulation (e.g., fetalnucleic acid) that can be used with a method described herein includemassively parallel signature sequencing (MPSS) approaches. MPSStypically is a solid phase method that uses adapter (i.e., tag)ligation, followed by adapter decoding, and reading of the nucleic acidsequence in small increments. Tagged PCR products are typicallyamplified such that each nucleic acid generates a PCR product with aunique tag. Tags are often used to attach the PCR products tomicrobeads. After several rounds of ligation-based sequencedetermination, for example, a sequence signature can be identified fromeach bead. Each signature sequence (MPSS tag) in a MPSS dataset isanalyzed, compared with all other signatures, and all identicalsignatures are counted.

In some embodiments, certain MPSS-based enrichment methods can includeamplification (e.g., PCR)-based approaches. In some embodiments,loci-specific amplification methods can be used (e.g., usingloci-specific amplification primers). In some embodiments, a multiplexSNP allele PCR approach can be used. In some embodiments, a multiplexSNP allele PCR approach can be used in combination with uniplexsequencing. For example, such an approach can involve the use ofmultiplex PCR (e.g., MASSARRAY system) and incorporation of captureprobe sequences into the amplicons followed by sequencing using, forexample, the Illumina MPSS system. In some embodiments, a multiplex SNPallele PCR approach can be used in combination with a three-primersystem and indexed sequencing. For example, such an approach can involvethe use of multiplex PCR (e.g., MASSARRAY system) with primers having afirst capture probe incorporated into certain loci-specific forward PCRprimers and adapter sequences incorporated into loci-specific reversePCR primers, to thereby generate amplicons, followed by a secondary PCRto incorporate reverse capture sequences and molecular index barcodesfor sequencing using, for example, the Illumina MPSS system. In someembodiments, a multiplex SNP allele PCR approach can be used incombination with a four-primer system and indexed sequencing. Forexample, such an approach can involve the use of multiplex PCR (e.g.,MASSARRAY system) with primers having adaptor sequences incorporatedinto both loci-specific forward and loci-specific reverse PCR primers,followed by a secondary PCR to incorporate both forward and reversecapture sequences and molecular index barcodes for sequencing using, forexample, the Illumina MPSS system. In some embodiments, a microfluidicsapproach can be used. In some embodiments, an array-based microfluidicsapproach can be used. For example, such an approach can involve the useof a microfluidics array (e.g., Fluidigm) for amplification at low plexand incorporation of index and capture probes, followed by sequencing.In some embodiments, an emulsion microfluidics approach can be used,such as, for example, digital droplet PCR.

In some embodiments, universal amplification methods can be used (e.g.,using universal or non-loci-specific amplification primers). In someembodiments, universal amplification methods can be used in combinationwith pull-down approaches. In some embodiments, a method can includebiotinylated ultramer pull-down (e.g., biotinylated pull-down assaysfrom Agilent or IDT) from a universally amplified sequencing library.For example, such an approach can involve preparation of a standardlibrary, enrichment for selected regions by a pull-down assay, and asecondary universal amplification step. In some embodiments, pull-downapproaches can be used in combination with ligation-based methods. Insome embodiments, a method can include biotinylated ultramer pull downwith sequence specific adapter ligation (e.g., HALOPLEX PCR, HaloGenomics). For example, such an approach can involve the use of selectorprobes to capture restriction enzyme-digested fragments, followed byligation of captured products to an adaptor, and universal amplificationfollowed by sequencing. In some embodiments, pull-down approaches can beused in combination with extension and ligation-based methods. In someembodiments, a method can include molecular inversion probe (MIP)extension and ligation. For example, such an approach can involve theuse of molecular inversion probes in combination with sequence adaptersfollowed by universal amplification and sequencing. In some embodiments,complementary DNA can be synthesized and sequenced withoutamplification.

In some embodiments, extension and ligation approaches can be performedwithout a pull-down component. In some embodiments, a method can includeloci-specific forward and reverse primer hybridization, extension andligation. Such methods can further include universal amplification orcomplementary DNA synthesis without amplification, followed bysequencing. Such methods can reduce or exclude background sequencesduring analysis, in some embodiments.

In some embodiments, pull-down approaches can be used with an optionalamplification component or with no amplification component. In someembodiments, a method can include a modified pull-down assay andligation with full incorporation of capture probes without universalamplification. For example, such an approach can involve the use ofmodified selector probes to capture restriction enzyme-digestedfragments, followed by ligation of captured products to an adaptor,optional amplification, and sequencing. In some embodiments, a methodcan include a biotinylated pull-down assay with extension and ligationof adaptor sequence in combination with circular single strandedligation. For example, such an approach can involve the use of selectorprobes to capture regions of interest (i.e., target sequences),extension of the probes, adaptor ligation, single stranded circularligation, optional amplification, and sequencing. In some embodiments,the analysis of the sequencing result can separate target sequences formbackground.

In some embodiments, nucleic acid is enriched for fragments from aselect genomic region (e.g., chromosome) using one or moresequence-based separation methods described herein. Sequence-basedseparation generally is based on nucleotide sequences present in thefragments of interest (e.g., target and/or reference fragments) andsubstantially not present in other fragments of the sample or present inan insubstantial amount of the other fragments (e.g., 5% or less). Insome embodiments, sequence-based separation can generate separatedtarget fragments and/or separated reference fragments. Separated targetfragments and/or separated reference fragments typically are isolatedaway from the remaining fragments in the nucleic acid sample. In someembodiments, the separated target fragments and the separated referencefragments also are isolated away from each other (e.g., isolated inseparate assay compartments). In some embodiments, the separated targetfragments and the separated reference fragments are isolated together(e.g., isolated in the same assay compartment). In some embodiments,unbound fragments can be differentially removed or degraded or digested.

In some embodiments, a selective nucleic acid capture process is used toseparate target and/or reference fragments away from the nucleic acidsample. Commercially available nucleic acid capture systems include, forexample, Nimblegen sequence capture system (Roche NimbleGen, Madison,Wis.); Illumina BEADARRAY platform (Illumina, San Diego, Calif.);Affymetrix GENECHIP platform (Affymetrix, Santa Clara, Calif.); AgilentSureSelect Target Enrichment System (Agilent Technologies, Santa Clara,Calif.); and related platforms. Such methods typically involvehybridization of a capture oligonucleotide to a segment or all of thenucleotide sequence of a target or reference fragment and can includeuse of a solid phase (e.g., solid phase array) and/or a solution basedplatform. Capture oligonucleotides (sometimes referred to as “bait”) canbe selected or designed such that they preferentially hybridize tonucleic acid fragments from selected genomic regions or loci (e.g., oneof chromosomes 21, 18, 13, X or Y, or a reference chromosome).

In some embodiments, nucleic acid is enriched for a particular nucleicacid fragment length, range of lengths, or lengths under or over aparticular threshold or cutoff using one or more length-based separationmethods. For example, isolated cell-free nucleic having fragment lengthsof about 300 base pairs or less, about 200 base pairs or less or about150 base pairs or less can be enriched for fetal nucleic acid, incertain instances. Nucleic acid fragment length typically refers to thenumber of nucleotides in the fragment. Nucleic acid fragment length alsois sometimes referred to as nucleic acid fragment size. In someembodiments, a length-based separation method is performed withoutmeasuring lengths of individual fragments. In some embodiments, a lengthbased separation method is performed in conjunction with a method fordetermining length of individual fragments. In some embodiments,length-based separation refers to a size fractionation procedure whereall or part of the fractionated pool can be isolated (e.g., retained)and/or analyzed. Size fractionation procedures are known in the art(e.g., separation on an array, separation by a molecular sieve,separation by gel electrophoresis, separation by column chromatography(e.g., size-exclusion columns), and microfluidics-based approaches). Insome embodiments, length-based separation approaches can includefragment circularization, chemical treatment (e.g., formaldehyde,polyethylene glycol (PEG)), mass spectrometry and/or size-specificnucleic acid amplification, for example.

Certain length-based separation methods that can be used with methodsdescribed herein employ a selective sequence tagging approach, forexample. The term “sequence tagging” refers to incorporating arecognizable and distinct sequence into a nucleic acid or population ofnucleic acids. The term “sequence tagging” as used herein has adifferent meaning than the term “sequence tag” described later herein.In such sequence tagging methods, a fragment size species (e.g., shortfragments) nucleic acids are subjected to selective sequence tagging ina sample that includes long and short nucleic acids. Such methodstypically involve performing a nucleic acid amplification reaction usinga set of nested primers which include inner primers and outer primers.In some embodiments, one or both of the inner can be tagged to therebyintroduce a tag onto the target amplification product. The outer primersgenerally do not anneal to the short fragments that carry the (inner)target sequence. The inner primers can anneal to the short fragments andgenerate an amplification product that carries a tag and the targetsequence. Typically, tagging of the long fragments is inhibited througha combination of mechanisms which include, for example, blockedextension of the inner primers by the prior annealing and extension ofthe outer primers. Enrichment for tagged fragments can be accomplishedby any of a variety of methods, including for example, exonucleasedigestion of single stranded nucleic acid and amplification of thetagged fragments using amplification primers specific for at least onetag.

Another length-based separation method that can be used with methodsdescribed herein involves subjecting a nucleic acid sample topolyethylene glycol (PEG) precipitation. Examples of methods includethose described in International Patent Application Publication Nos.WO2007/140417 and WO2010/115016. This method in general entailscontacting a nucleic acid sample with PEG in the presence of one or moremonovalent salts under conditions sufficient to substantiallyprecipitate large nucleic acids without substantially precipitatingsmall (e.g., less than 300 nucleotides) nucleic acids.

Another size-based enrichment method that can be used with methodsdescribed herein involves circularization by ligation, for example,using circligase. Short nucleic acid fragments typically can becircularized with higher efficiency than long fragments.Non-circularized sequences can be separated from circularized sequences,and the enriched short fragments can be used for further analysis.

Determining Fetal Nucleic Acid Content

The amount of fetal nucleic acid (e.g., concentration, relative amount,absolute amount, copy number, and the like) in nucleic acid isdetermined in some embodiments. In some embodiments, the amount of fetalnucleic acid in a sample is referred to as “fetal fraction”. In someembodiments, “fetal fraction” refers to the fraction of fetal nucleicacid in circulating cell-free nucleic acid in a sample (e.g., a bloodsample, a serum sample, a plasma sample) obtained from a pregnantfemale. In some embodiments, a method in which a genetic variation isdetermined also can comprise determining fetal fraction. Determiningfetal fraction can be performed in a suitable manner, non-limitingexamples of which include methods described below.

In some embodiments, the amount of fetal nucleic acid is determinedaccording to markers specific to a male fetus (e.g., Y-chromosome STRmarkers (e.g., DYS 19, DYS 385, DYS 392 markers); RhD marker inRhD-negative females), allelic ratios of polymorphic sequences, oraccording to one or more markers specific to fetal nucleic acid and notmaternal nucleic acid (e.g., differential epigenetic biomarkers (e.g.,methylation; described in further detail below) between mother andfetus, or fetal RNA markers in maternal blood plasma (see e.g., Lo,2005, Journal of Histochemistry and Cytochemistry 53 (3): 293-296)).

Determination of fetal nucleic acid content (e.g., fetal fraction)sometimes is performed using a fetal quantifier assay (FQA) asdescribed, for example, in U.S. Patent Application Publication No.2010/0105049, which is hereby incorporated by reference. This type ofassay allows for the detection and quantification of fetal nucleic acidin a maternal sample based on the methylation status of the nucleic acidin the sample. The amount of fetal nucleic acid from a maternal samplesometimes can be determined relative to the total amount of nucleic acidpresent, thereby providing the percentage of fetal nucleic acid in thesample. The copy number of fetal nucleic acid sometimes can bedetermined in a maternal sample. The amount of fetal nucleic acidsometimes can be determined in a sequence-specific (or locus-specific)manner and sometimes with sufficient sensitivity to allow for accuratechromosomal dosage analysis (for example, to detect the presence orabsence of a fetal aneuploidy or other genetic variation).

A fetal quantifier assay (FQA) can be performed in conjunction with anymethod described herein. Such an assay can be performed by any methodknown in the art and/or described in U.S. Patent Application PublicationNo. 2010/0105049, such as, for example, by a method that can distinguishbetween maternal and fetal DNA based on differential methylation status,and quantify (i.e. determine the amount of) the fetal DNA. Methods fordifferentiating nucleic acid based on methylation status include, butare not limited to, methylation sensitive capture, for example, using aMBD2-Fc fragment in which the methyl binding domain of MBD2 is fused tothe Fc fragment of an antibody (MBD-FC) (Gebhard et al. (2006) CancerRes. 66(12):6118-28); methylation specific antibodies; bisulfiteconversion methods, for example, MSP (methylation-sensitive PCR), COBRA,methylation-sensitive single nucleotide primer extension (Ms-SNuPE) orSequenom MassCLEAVE™ technology; and the use of methylation sensitiverestriction enzymes (e.g., digestion of maternal DNA in a maternalsample using one or more methylation sensitive restriction enzymesthereby enriching the fetal DNA). Methyl-sensitive enzymes also can beused to differentiate nucleic acid based on methylation status, which,for example, can preferentially or substantially cleave or digest attheir DNA recognition sequence if the latter is non-methylated. Thus, anunmethylated DNA sample will be cut into smaller fragments than amethylated DNA sample and a hypermethylated DNA sample will not becleaved. Except where explicitly stated, any method for differentiatingnucleic acid based on methylation status can be used with thecompositions and methods of the technology herein. The amount of fetalDNA can be determined, for example, by introducing one or morecompetitors at known concentrations during an amplification reaction.Determining the amount of fetal DNA also can be done, for example, byRT-PCR, primer extension, sequencing and/or counting. In certaininstances, the amount of nucleic acid can be determined using BEAMingtechnology as described in U.S. Patent Application Publication No.2007/0065823. In some embodiments, the restriction efficiency can bedetermined and the efficiency rate is used to further determine theamount of fetal DNA.

A fetal quantifier assay (FQA) sometimes can be used to determine theconcentration of fetal DNA in a maternal sample, for example, by thefollowing method: a) determine the total amount of DNA present in amaternal sample; b) selectively digest the maternal DNA in a maternalsample using one or more methylation sensitive restriction enzymesthereby enriching the fetal DNA; c) determine the amount of fetal DNAfrom step b); and d) compare the amount of fetal DNA from step c) to thetotal amount of DNA from step a), thereby determining the concentrationof fetal DNA in the maternal sample. The absolute copy number of fetalnucleic acid in a maternal sample sometimes can be determined, forexample, using mass spectrometry and/or a system that uses a competitivePCR approach for absolute copy number measurements. See for example,Ding and Cantor (2003) Proc.Natl.Acad.Sci. USA 100:3059-3064, and U.S.Patent Application Publication No. 2004/0081993, both of which arehereby incorporated by reference.

Fetal fraction sometimes can be determined based on allelic ratios ofpolymorphic sequences (e.g., single nucleotide polymorphisms (SNPs)),such as, for example, using a method described in U.S. PatentApplication Publication No. 2011/0224087, which is hereby incorporatedby reference. In such a method, nucleotide sequence reads are obtainedfor a maternal sample and fetal fraction is determined by comparing thetotal number of nucleotide sequence reads that map to a first allele andthe total number of nucleotide sequence reads that map to a secondallele at an informative polymorphic site (e.g., SNP) in a referencegenome. Fetal alleles can be identified, for example, by their relativeminor contribution to the mixture of fetal and maternal nucleic acids inthe sample when compared to the major contribution to the mixture by thematernal nucleic acids. Accordingly, the relative abundance of fetalnucleic acid in a maternal sample can be determined as a parameter ofthe total number of unique sequence reads mapped to a target nucleicacid sequence on a reference genome for each of the two alleles of apolymorphic site.

The amount of fetal nucleic acid in extracellular nucleic acid can bequantified and used in conjunction with a method provided herein. Thus,in certain embodiments, methods of the technology described hereincomprise an additional step of determining the amount of fetal nucleicacid. The amount of fetal nucleic acid can be determined in a nucleicacid sample from a subject before or after processing to prepare samplenucleic acid. In certain embodiments, the amount of fetal nucleic acidis determined in a sample after sample nucleic acid is processed andprepared, which amount is utilized for further assessment. In someembodiments, an outcome comprises factoring the fraction of fetalnucleic acid in the sample nucleic acid (e.g., adjusting counts,removing samples, making a call or not making a call).

The determination step can be performed before, during, at any one pointin a method described herein, or after certain (e.g., aneuploidydetection) methods described herein. For example, to achieve ananeuploidy determination method with a given sensitivity or specificity,a fetal nucleic acid quantification method may be implemented prior to,during or after aneuploidy determination to identify those samples withgreater than about 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%,14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25% or more fetalnucleic acid. In some embodiments, samples determined as having acertain threshold amount of fetal nucleic acid (e.g., about 15% or morefetal nucleic acid; about 4% or more fetal nucleic acid) are furtheranalyzed for the presence or absence of aneuploidy or genetic variation,for example. In certain embodiments, determinations of, for example, thepresence or absence of aneuploidy are selected (e.g., selected andcommunicated to a patient) only for samples having a certain thresholdamount of fetal nucleic acid (e.g., about 15% or more fetal nucleicacid; about 4% or more fetal nucleic acid).

In some embodiments, the determination of fetal fraction or determiningthe amount of fetal nucleic acid is not required or necessary foridentifying the presence or absence of a chromosome aneuploidy. In someembodiments, identifying the presence or absence of a chromosomeaneuploidy does not require the sequence differentiation of fetal versusmaternal DNA. This is because the summed contribution of both maternaland fetal sequences in a particular chromosome, chromosome portion orsegment thereof is analyzed, in some embodiments. In some embodiments,identifying the presence or absence of a chromosome aneuploidy does notrely on a priori sequence information that would distinguish fetal DNAfrom maternal DNA.

Obtaining Sequence Reads

Sequence reads can be obtained from enriched samples. Sequencing,mapping and related analytical methods are known in the art (e.g.,United States Patent Application Publication US2009/0029377,incorporated by reference). Certain aspects of such processes aredescribed hereafter.

As used herein, “reads” are short nucleotide sequences produced by anysequencing process described herein or known in the art. Reads can begenerated from one end of nucleic acid fragments (“single-end reads”),and sometimes are generated from both ends of nucleic acids (“double-endreads”). In certain embodiments, “obtaining” nucleic acid sequence readsof a sample from a subject and/or “obtaining” nucleic acid sequencereads of a biological specimen from one or more reference persons caninvolve directly sequencing nucleic acid to obtain the sequenceinformation. In some embodiments, “obtaining” can involve receivingsequence information obtained directly from a nucleic acid by another.

In some embodiments, one nucleic acid sample from one individual issequenced. In certain embodiments, nucleic acid samples from two or morebiological samples, where each biological sample is from one individualor two or more individuals, are pooled and the pool is sequenced. In thelatter embodiments, a nucleic acid sample from each biological sampleoften is identified by one or more unique identification tags.

In some embodiments, a fraction of the genome is sequenced, whichsometimes is expressed in the amount of the genome covered by thedetermined nucleotide sequences (e.g., “fold” coverage less than 1).When a genome is sequenced with about 1-fold coverage, roughly 100% ofthe nucleotide sequence of the genome is represented by reads. A genomealso can be sequenced with redundancy, where a given region of thegenome can be covered by two or more reads or overlapping reads (e.g.,“fold” coverage greater than 1). In some embodiments, a genome issequenced with about 0.1-fold to about 100-fold coverage, about 0.2-foldto 20-fold coverage, or about 0.2-fold to about 1-fold coverage (e.g.,about 0.2-, 0.3-, 0.4-, 0.5-, 0.6-, 0.7-, 0.8-, 0.9-, 1-, 2-, 3-, 4-,5-, 6-, 7-, 8-, 9-, 10-, 15-, 20-, 30-, 40-, 50-, 60-, 70-, 80-, 90-foldcoverage).

In certain embodiments, a fraction of a nucleic acid pool that issequenced in a run is further sub-selected prior to sequencing. Incertain embodiments, hybridization-based techniques (e.g., usingoligonucleotide arrays) can be used to first sub-select for nucleic acidsequences from certain chromosomes (e.g., a potentially aneuploidchromosome and other chromosome(s) not involved in the aneuploidytested). In some embodiments, nucleic acid can be fractionated by size(e.g., by gel electrophoresis, size exclusion chromatography or bymicrofluidics-based approach) and in certain instances, fetal nucleicacid can be enriched by selecting for nucleic acid having a lowermolecular weight (e.g., less than 300 base pairs, less than 200 basepairs, less than 150 base pairs, less than 100 base pairs). In someembodiments, fetal nucleic acid can be enriched by suppressing maternalbackground nucleic acid, such as by the addition of formaldehyde. Insome embodiments, a portion or subset of a pre-selected pool of nucleicacids is sequenced randomly. In some embodiments, the nucleic acid isamplified prior to sequencing. In some embodiments, a portion or subsetof the nucleic acid is amplified prior to sequencing.

Any sequencing method suitable for conducting methods described hereincan be utilized. In some embodiments, a high-throughput sequencingmethod is used. High-throughput sequencing methods generally involveclonally amplified DNA templates or single DNA molecules that aresequenced in a massively parallel fashion within a flow cell (e.g. asdescribed in Metzker M Nature Rev 11:31-46 (2010); Volkerding et al.Clin Chem 55:641-658 (2009)). Such sequencing methods also can providedigital quantitative information, where each sequence read is acountable “sequence tag” representing an individual clonal DNA templateor a single DNA molecule. High-throughput sequencing technologiesinclude, for example, sequencing-by-synthesis with reversible dyeterminators, sequencing by oligonucleotide probe ligation,pyrosequencing and real time sequencing.

Systems utilized for high-throughput sequencing methods are commerciallyavailable and include, for example, the Roche 454 platform, the AppliedBiosystems SOLID platform, the Helicos True Single Molecule DNAsequencing technology, the sequencing-by-hybridization platform fromAffymetrix Inc., the single molecule, real-time (SMRT) technology ofPacific Biosciences, the sequencing-by-synthesis platforms from 454 LifeSciences, Illumina/Solexa and Helicos Biosciences, and thesequencing-by-ligation platform from Applied Biosystems. The ION TORRENTtechnology from Life technologies and nanopore sequencing also can beused in high-throughput sequencing approaches.

In some embodiments, first generation technology, such as, for example,Sanger sequencing including the automated Sanger sequencing, can be usedin the methods provided herein. Additional sequencing technologies thatinclude the use of developing nucleic acid imaging technologies (e.g.transmission electron microscopy (TEM) and atomic force microscopy(AFM)), are also contemplated herein. Examples of various sequencingtechnologies are described below.

A nucleic acid sequencing technology that may be used in the methodsdescribed herein is sequencing-by-synthesis and reversibleterminator-based sequencing (e.g. Illumina's Genome Analyzer and GenomeAnalyzer II). With this technology, millions of nucleic acid (e.g. DNA)fragments can be sequenced in parallel. In one example of this type ofsequencing technology, a flow cell is used which contains an opticallytransparent slide with 8 individual lanes on the surfaces of which arebound oligonucleotide anchors. Template DNA often is fragmented intolengths of several hundred base pairs and end-repaired to generate5′-phosphorylated blunt ends and a single adenine (A) base is then addedto the 3′ end of the blunt phosphorylated DNA fragments. This additionprepares the DNA fragments for ligation to oligonucleotide adapters,which have an overhang of a single thymine (T) base at their 3′ end toincrease ligation efficiency. The adapter oligonucleotides arecomplementary to the flow-cell anchors. Under limiting-dilutionconditions, adapter-modified, single-stranded template DNA is added tothe flow cell and immobilized by hybridization to the anchors. Incontrast to emulsion PCR, DNA templates are amplified in the flow cellby “bridge” amplification, which relies on captured DNA strands“arching” over and hybridizing to an adjacent anchor oligonucleotide.Multiple amplification cycles convert the single-molecule DNA templateto a clonally amplified arching “cluster,” with each cluster containingapproximately 1000 clonal molecules. Approximately 50×10⁶ separateclusters can be generated per flow cell. For sequencing, the clustersare denatured, and a subsequent chemical cleavage reaction and washleave only forward strands for single-end sequencing. Sequencing of theforward strands is initiated by hybridizing a primer complementary tothe adapter sequences, which is followed by addition of polymerase and amixture of four differently colored fluorescent reversible dyeterminators. The terminators are incorporated according to sequencecomplementarity in each strand in a clonal cluster. After incorporation,excess reagents are washed away, the clusters are opticallyinterrogated, and the fluorescence is recorded. With successive chemicalsteps, the reversible dye terminators are unblocked, the fluorescentlabels are cleaved and washed away, and the next sequencing cycle isperformed. This iterative, sequencing-by-synthesis process sometimesrequires approximately 2.5 days to generate read lengths of 36 bases.With 50×10⁶ clusters per flow cell, the overall sequence output can begreater than 1 billion base pairs (Gb) per analytical run.

Another nucleic acid sequencing technology that may be used with themethods described herein is 454 sequencing (Roche). 454 sequencing usesa large-scale parallel pyrosequencing system capable of sequencing about400-600 megabases of DNA per run. The process typically involves twosteps. In the first step, sample nucleic acid (e.g. DNA) is sometimesfractionated into smaller fragments (300-800 base pairs) and polished(made blunt at each end). Short adaptors are then ligated onto the endsof the fragments. These adaptors provide priming sequences for bothamplification and sequencing of the sample-library fragments. Oneadaptor (Adaptor B) contains a 5′-biotin tag for immobilization of theDNA library onto streptavidin-coated beads. After nick repair, thenon-biotinylated strand is released and used as a single-strandedtemplate DNA (sstDNA) library. The sstDNA library is assessed for itsquality and the optimal amount (DNA copies per bead) needed for emPCR isdetermined by titration. The sstDNA library is immobilized onto beads.The beads containing a library fragment carry a single sstDNA molecule.The bead-bound library is emulsified with the amplification reagents ina water-in-oil mixture. Each bead is captured within its ownmicroreactor where PCR amplification occurs. This results inbead-immobilized, clonally amplified DNA fragments.

In the second step of 454 sequencing, single-stranded template DNAlibrary beads are added to an incubation mix containing DNA polymeraseand are layered with beads containing sulfurylase and luciferase onto adevice containing pico-liter sized wells. Pyrosequencing is performed oneach DNA fragment in parallel. Addition of one or more nucleotidesgenerates a light signal that is recorded by a CCD camera in asequencing instrument. The signal strength is proportional to the numberof nucleotides incorporated. Pyrosequencing exploits the release ofpyrophosphate (PPi) upon nucleotide addition. PPi is converted to ATP byATP sulfurylase in the presence of adenosine 5′ phosphosulfate.Luciferase uses ATP to convert luciferin to oxyluciferin, and thisreaction generates light that is discerned and analyzed (see, forexample, Margulies, M. et al. Nature 437:376-380 (2005)).

Another nucleic acid sequencing technology that may be used in themethods provided herein is Applied Biosystems' SOLiD™ technology. InSOLiD™ sequencing-by-ligation, a library of nucleic acid fragments isprepared from the sample and is used to prepare clonal bead populations.With this method, one species of nucleic acid fragment will be presenton the surface of each bead (e.g. magnetic bead). Sample nucleic acid(e.g. genomic DNA) is sheared into fragments, and adaptors aresubsequently attached to the 5′ and 3′ ends of the fragments to generatea fragment library. The adapters are typically universal adaptersequences so that the starting sequence of every fragment is both knownand identical. Emulsion PCR takes place in microreactors containing allthe necessary reagents for PCR. The resulting PCR products attached tothe beads are then covalently bound to a glass slide. Primers thenhybridize to the adapter sequence within the library template. A set offour fluorescently labeled di-base probes compete for ligation to thesequencing primer. Specificity of the di-base probe is achieved byinterrogating every 1st and 2nd base in each ligation reaction. Multiplecycles of ligation, detection and cleavage are performed with the numberof cycles determining the eventual read length. Following a series ofligation cycles, the extension product is removed and the template isreset with a primer complementary to the n-1 position for a second roundof ligation cycles. Often, five rounds of primer reset are completed foreach sequence tag. Through the primer reset process, each base isinterrogated in two independent ligation reactions by two differentprimers. For example, the base at read position 5 is assayed by primernumber 2 in ligation cycle 2 and by primer number 3 in ligation cycle 1.

Another nucleic acid sequencing technology that may be used in themethods described herein is the Helicos True Single Molecule Sequencing(tSMS). In the tSMS technique, a polyA sequence is added to the 3′ endof each nucleic acid (e.g. DNA) strand from the sample. Each strand islabeled by the addition of a fluorescently labeled adenosine nucleotide.The DNA strands are then hybridized to a flow cell, which containsmillions of oligo-T capture sites that are immobilized to the flow cellsurface. The templates can be at a density of about 100 milliontemplates/cm². The flow cell is then loaded into a sequencing apparatusand a laser illuminates the surface of the flow cell, revealing theposition of each template. A CCD camera can map the position of thetemplates on the flow cell surface. The template fluorescent label isthen cleaved and washed away. The sequencing reaction begins byintroducing a DNA polymerase and a fluorescently labeled nucleotide. Theoligo-T nucleic acid serves as a primer. The polymerase incorporates thelabeled nucleotides to the primer in a template directed manner. Thepolymerase and unincorporated nucleotides are removed. The templatesthat have directed incorporation of the fluorescently labeled nucleotideare detected by imaging the flow cell surface. After imaging, a cleavagestep removes the fluorescent label, and the process is repeated withother fluorescently labeled nucleotides until the desired read length isachieved. Sequence information is collected with each nucleotideaddition step (see, for example, Harris T. D. et al., Science320:106-109 (2008)).

Another nucleic acid sequencing technology that may be used in themethods provided herein is the single molecule, real-time (SMRT™)sequencing technology of Pacific Biosciences. With this method, each ofthe four DNA bases is attached to one of four different fluorescentdyes. These dyes are phospholinked. A single DNA polymerase isimmobilized with a single molecule of template single stranded DNA atthe bottom of a zero-mode waveguide (ZMW). A ZMW is a confinementstructure which enables observation of incorporation of a singlenucleotide by DNA polymerase against the background of fluorescentnucleotides that rapidly diffuse in an out of the ZMW (in microseconds).It takes several milliseconds to incorporate a nucleotide into a growingstrand. During this time, the fluorescent label is excited and producesa fluorescent signal, and the fluorescent tag is cleaved off. Detectionof the corresponding fluorescence of the dye indicates which base wasincorporated. The process is then repeated.

Another nucleic acid sequencing technology that may be used in themethods described herein is ION TORRENT (Life Technologies) singlemolecule sequencing which pairs semiconductor technology with a simplesequencing chemistry to directly translate chemically encodedinformation (A, C, G, T) into digital information (0, 1) on asemiconductor chip. ION TORRENT uses a high-density array ofmicro-machined wells to perform nucleic acid sequencing in a massivelyparallel way. Each well holds a different DNA molecule. Beneath thewells is an ion-sensitive layer and beneath that an ion sensor.Typically, when a nucleotide is incorporated into a strand of DNA by apolymerase, a hydrogen ion is released as a byproduct. If a nucleotide,for example a C, is added to a DNA template and is then incorporatedinto a strand of DNA, a hydrogen ion will be released. The charge fromthat ion will change the pH of the solution, which can be detected by anion sensor. A sequencer can call the base, going directly from chemicalinformation to digital information. The sequencer then sequentiallyfloods the chip with one nucleotide after another. If the nextnucleotide that floods the chip is not a match, no voltage change willbe recorded and no base will be called. If there are two identical baseson the DNA strand, the voltage will be double, and the chip will recordtwo identical bases called. Because this is direct detection (i.e.detection without scanning, cameras or light), each nucleotideincorporation is recorded in seconds.

Another nucleic acid sequencing technology that may be used in themethods described herein is the chemical-sensitive field effecttransistor (CHEMFET) array. In one example of this sequencing technique,DNA molecules are placed into reaction chambers, and the templatemolecules can be hybridized to a sequencing primer bound to apolymerase. Incorporation of one or more triphosphates into a newnucleic acid strand at the 3′ end of the sequencing primer can bedetected by a change in current by a CHEMFET sensor. An array can havemultiple CHEMFET sensors. In another example, single nucleic acids areattached to beads, and the nucleic acids can be amplified on the bead,and the individual beads can be transferred to individual reactionchambers on a CHEMFET array, with each chamber having a CHEMFET sensor,and the nucleic acids can be sequenced (see, for example, U.S. PatentPublication No. 2009/0026082).

Another nucleic acid sequencing technology that may be used in themethods described herein is electron microscopy. In one example of thissequencing technique, individual nucleic acid (e.g. DNA) molecules arelabeled using metallic labels that are distinguishable using an electronmicroscope. These molecules are then stretched on a flat surface andimaged using an electron microscope to measure sequences (see, forexample, Moudrianakis E. N. and Beer M. Proc Natl Acad Sci USA. 1965March; 53:564-71). In some instances, transmission electron microscopy(TEM) is used (e.g. Halcyon Molecular's TEM method). This method, termedIndividual Molecule Placement Rapid Nano Transfer (IMPRNT), includesutilizing single atom resolution transmission electron microscopeimaging of high-molecular weight (e.g. about 150 kb or greater) DNAselectively labeled with heavy atom markers and arranging thesemolecules on ultra-thin films in ultra-dense (3 nm strand-to-strand)parallel arrays with consistent base-to-base spacing. The electronmicroscope is used to image the molecules on the films to determine theposition of the heavy atom markers and to extract base sequenceinformation from the DNA (see, for example, PCT patent publication WO2009/046445).

Other sequencing methods that may be used to conduct methods hereininclude digital PCR and sequencing by hybridization. Digital polymerasechain reaction (digital PCR or dPCR) can be used to directly identifyand quantify nucleic acids in a sample. Digital PCR can be performed inan emulsion, in some embodiments. For example, individual nucleic acidsare separated, e.g., in a microfluidic chamber device, and each nucleicacid is individually amplified by PCR. Nucleic acids can be separatedsuch that there is no more than one nucleic acid per well. In someembodiments, different probes can be used to distinguish various alleles(e.g. fetal alleles and maternal alleles). Alleles can be enumerated todetermine copy number. In sequencing by hybridization, the methodinvolves contacting a plurality of polynucleotide sequences with aplurality of polynucleotide probes, where each of the plurality ofpolynucleotide probes can be optionally tethered to a substrate. Thesubstrate can be a flat surface with an array of known nucleotidesequences, in some embodiments. The pattern of hybridization to thearray can be used to determine the polynucleotide sequences present inthe sample. In some embodiments, each probe is tethered to a bead, e.g.,a magnetic bead or the like. Hybridization to the beads can beidentified and used to identify the plurality of polynucleotidesequences within the sample.

In some embodiments, nanopore sequencing can be used in the methodsdescribed herein. Nanopore sequencing is a single-molecule sequencingtechnology whereby a single nucleic acid molecule (e.g. DNA) issequenced directly as it passes through a nanopore. A nanopore is asmall hole or channel, of the order of 1 nanometer in diameter. Certaintransmembrane cellular proteins can act as nanopores (e.g.alpha-hemolysin). Nanopores sometimes can be synthesized (e.g. using asilicon platform). Immersion of a nanopore in a conducting fluid andapplication of a potential across it results in a slight electricalcurrent due to conduction of ions through the nanopore. The amount ofcurrent which flows is sensitive to the size of the nanopore. As a DNAmolecule passes through a nanopore, each nucleotide on the DNA moleculeobstructs the nanopore to a different degree and generatescharacteristic changes to the current. The amount of current which canpass through the nanopore at any given moment therefore varies dependingon whether the nanopore is blocked by an A, a C, a G, a T, or in someinstances, methyl-C. The change in the current through the nanopore asthe DNA molecule passes through the nanopore represents a direct readingof the DNA sequence. In some instances a nanopore can be used toidentify individual DNA bases as they pass through the nanopore in thecorrect order (see, for example, Soni G V and Meller A. Clin Chem 53:1996-2001 (2007); PCT publication no. WO2010/004265).

There are a number of ways that nanopores can be used to sequencenucleic acid molecules. In some embodiments, an exonuclease enzyme, suchas a deoxyribonuclease, is used. In this case, the exonuclease enzyme isused to sequentially detach nucleotides from a nucleic acid (e.g. DNA)molecule. The nucleotides are then detected and discriminated by thenanopore in order of their release, thus reading the sequence of theoriginal strand. For such an embodiment, the exonuclease enzyme can beattached to the nanopore such that a proportion of the nucleotidesreleased from the DNA molecule is capable of entering and interactingwith the channel of the nanopore. The exonuclease can be attached to thenanopore structure at a site in close proximity to the part of thenanopore that forms the opening of the channel. In some instances, theexonuclease enzyme can be attached to the nanopore structure such thatits nucleotide exit trajectory site is orientated towards the part ofthe nanopore that forms part of the opening.

In some embodiments, nanopore sequencing of nucleic acids involves theuse of an enzyme that pushes or pulls the nucleic acid (e.g. DNA)molecule through the pore. In this case, the ionic current fluctuates asa nucleotide in the DNA molecule passes through the pore. Thefluctuations in the current are indicative of the DNA sequence. For suchan embodiment, the enzyme can be attached to the nanopore structure suchthat it is capable of pushing or pulling the target nucleic acid throughthe channel of a nanopore without interfering with the flow of ioniccurrent through the pore. The enzyme can be attached to the nanoporestructure at a site in close proximity to the part of the structure thatforms part of the opening. The enzyme can be attached to the subunit,for example, such that its active site is orientated towards the part ofthe structure that forms part of the opening.

In some embodiments, nanopore sequencing of nucleic acids involvesdetection of polymerase bi-products in close proximity to a nanoporedetector. In this case, nucleoside phosphates (nucleotides) are labeledso that a phosphate labeled species is released upon the addition of apolymerase to the nucleotide strand and the phosphate labeled species isdetected by the pore. Typically, the phosphate species contains aspecific label for each nucleotide. As nucleotides are sequentiallyadded to the nucleic acid strand, the bi-products of the base additionare detected. The order that the phosphate labeled species are detectedcan be used to determine the sequence of the nucleic acid strand.

The length of the sequence read is often associated with the particularsequencing technology. High-throughput methods, for example, providesequence reads that can vary in size from tens to hundreds of base pairs(bp). Nanopore sequencing, for example, can provide sequence reads thatcan vary in size from tens to hundreds to thousands of base pairs. Insome embodiments, the sequence reads are of a mean, median or averagelength of about 15 bp to 900 bp long (e.g. about 20 bp, about 25 bp,about 30 bp, about 35 bp, about 40 bp, about 45 bp, about 50 bp, about55 bp, about 60 bp, about 65 bp, about 70 bp, about 75 bp, about 80 bp,about 85 bp, about 90 bp, about 95 bp, about 100 bp, about 110 bp, about120 bp, about 130, about 140 bp, about 150 bp, about 200 bp, about 250bp, about 300 bp, about 350 bp, about 400 bp, about 450 bp, or about 500bp. In some embodiments, the sequence reads are of a mean, median oraverage length of about 1000 bp or more.

In some embodiments, nucleic acids may include a fluorescent signal orsequence tag information. Quantification of the signal or tag may beused in a variety of techniques such as, for example, flow cytometry,quantitative polymerase chain reaction (qPCR), gel electrophoresis,gene-chip analysis, microarray, mass spectrometry, cytofluorimetricanalysis, fluorescence microscopy, confocal laser scanning microscopy,laser scanning cytometry, affinity chromatography, manual batch modeseparation, electric field suspension, sequencing, and combinationthereof.

Mapping Reads

Mapping nucleotide sequence reads (i.e., sequence information from afragment whose physical genomic position is unknown) can be performed ina number of ways, and often comprises alignment of the obtained sequencereads with a matching sequence in a reference genome (e.g., Li et al.,“Mapping short DNA sequencing reads and calling variants using mappingquality score,” Genome Res., 2008 Aug. 19.) In such alignments, sequencereads generally are aligned to a reference sequence and those that alignare designated as being “mapped” or a “sequence tag.” In someembodiments, a mapped sequence read is referred to as a “hit”. In someembodiments, mapped sequence reads are grouped together according tovarious parameters and assigned to particular genome sections, which arediscussed in further detail below.

Various computational methods can be used to map each sequence read to agenome section. Non-limiting examples of computer algorithms that can beused to align sequences include BLAST, BLITZ, and FASTA, or variationsthereof. In some embodiments, the sequence reads can be found and/oraligned with sequences in nucleic acid databases known in the artincluding, for example, GenBank, dbEST, dbSTS, EMBL (European MolecularBiology Laboratory) and DDBJ (DNA Databank of Japan). BLAST or similartools can be used to search the identified sequences against a sequencedatabase. Search hits can then be used to sort the identified sequencesinto appropriate genome sections (described hereafter), for example.

A “sequence tag” is a nucleic acid (e.g. DNA) sequence (i.e. read)assigned specifically to a particular genome section and/or chromosome(i.e. one of chromosomes 1-22, X or Y for a human subject). A sequencetag may be repetitive or non-repetitive within a single portion of thereference genome (e.g., a chromosome). In some embodiments, repetitivesequence tags are eliminated from further analysis (e.g.quantification). In some embodiments, a read may uniquely ornon-uniquely map to portions in the reference genome. A read isconsidered “uniquely mapped” if it aligns with a single sequence in thereference genome. A read is considered “non-uniquely mapped” if italigns with two or more sequences in the reference genome. In someembodiments, non-uniquely mapped reads are eliminated from furtheranalysis (e.g. quantification). A certain, small degree of mismatch(0-1) may be allowed to account for single nucleotide polymorphisms thatmay exist between the reference genome and the reads from individualsamples being mapped, in certain embodiments. In some embodiments, nodegree of mismatch is allowed for a read mapped to a reference sequence.

As used herein, a reference sequence or reference genome often is anassembled or partially assembled genomic sequence from an individual ormultiple individuals. In certain embodiments, where a sample nucleicacid is from a pregnant female, a reference sequence sometimes is notfrom the fetus, the mother of the fetus or the father of the fetus, andis referred to herein as an “external reference.” A maternal referencemay be prepared and used in some embodiments. When a reference from thepregnant female is prepared (“maternal reference sequence”) based on anexternal reference, reads from DNA of the pregnant female that containssubstantially no fetal DNA often are mapped to the external referencesequence and assembled. In certain embodiments the external reference isfrom DNA of an individual having substantially the same ethnicity as thepregnant female. A maternal reference sequence may not completely coverthe maternal genomic DNA (e.g., it may cover about 50%, 60%, 70%, 80%,90% or more of the maternal genomic DNA), and the maternal reference maynot perfectly match the maternal genomic DNA sequence (e.g., thematernal reference sequence may include multiple mismatches).

Genome Sections

In some embodiments, mapped sequence reads (i.e. sequence tags) aregrouped together according to various parameters and assigned toparticular genome sections. Often, the individual mapped sequence readscan be used to identify an amount of a genome section present in asample. In some embodiments, the amount of a genome section can beindicative of the amount of a larger sequence (e.g. a chromosome) in thesample. The term “genome section” can also be referred to herein as“sequence window”, “section”, “bin”, “locus”, “region”, “partition” or“segment”. In some embodiments, a genome section is an entirechromosome, portion of a chromosome, multiple chromosome portions,multiple chromosomes, portions from multiple chromosomes, and/orcombinations thereof. In some embodiments, a genome section isdelineated based on one or more parameters which include, for example,length or a particular feature or features of the sequence. In someembodiments, a genome section is based on a particular length of genomicsequence. In some embodiments, the methods include analysis of multiplemapped sequence reads to a plurality of genome sections. The genomesections can be approximately the same length or the genome sections canbe different lengths. In some embodiments, a genome section is about 10kilobases (kb) to about 100 kb, about 20 kb to about 80 kb, about 30 kbto about 70 kb, about 40 kb to about 60 kb, and sometimes about 50 kb.In some embodiments, the genome section is about 10 kb to about 20 kb.The genomic sections discussed herein are not limited to contiguous runsof sequence. Thus, genome sections can be made up of contiguous ornon-contiguous sequences. The genomic sections discussed herein are notlimited to a single chromosome and, in some embodiments, may transcendindividual chromosomes. In some embodiments, genomic sections may spanone, two, or more entire chromosomes. In addition, the genomic sectionsmay span joint or disjoint portions of multiple chromosomes.

In some embodiments, genome sections can be particular chromosomesections in a chromosome of interest, such as, for example, chromosomeswhere a genetic variation is assessed (e.g. an aneuploidy of chromosomes13, 18 and/or 21). A genome section can also be a pathogenic genome(e.g. bacterial, fungal or viral) or fragment thereof. Genome sectionscan be genes, gene fragments, regulatory sequences, introns, exons, andthe like.

In some embodiments, a genome (e.g. human genome) is partitioned intogenome sections based on the information content of the regions. Theresulting genomic regions may contain sequences for multiple chromosomesand/or may contain sequences for portions of multiple chromosomes.

In some embodiments, the partitioning may eliminate similar locationsacross the genome and only keep unique regions. The eliminated regionsmay be within a single chromosome or may span multiple chromosomes. Theresulting genome is thus trimmed down and optimized for fasteralignment, often allowing for focus on uniquely identifiable sequences.In some embodiments, the partitioning may down weight similar regions.The process for down weighting a genome section is discussed in furtherdetail below. In some embodiments, the partitioning of the genome intoregions transcending chromosomes may be based on information gainproduced in the context of classification. For example, the informationcontent may be quantified using the p-value profile measuring thesignificance of particular genomic locations for distinguishing betweengroups of confirmed normal and abnormal subjects (e.g. euploid andtrisomy subjects). In some embodiments, the partitioning of the genomeinto regions transcending chromosomes may be based on any othercriterion, such as, for example, speed/convenience while aligning tags,high or low GC content, uniformity of GC content, other measures ofsequence content (e.g. fraction of individual nucleotides, fraction ofpyrimidines or purines, fraction of natural vs. non-natural nucleicacids, fraction of methylated nucleotides, and CpG content), methylationstate, duplex melting temperature, amenability to sequencing or PCR,level of uncertainty assigned to individual bins, and/or a targetedsearch for particular features.

Outcomes and Determination of the Presence or Absence of a GeneticVariation

Some genetic variations are associated with medical conditions. Geneticvariations often include a gain, a loss, and/or alteration (e.g.,reorganization or substitution) of genetic information (e.g.,chromosomes, portions of chromosomes, polymorphic regions, translocatedregions, altered nucleotide sequence, the like or combinations of theforegoing) that result in a detectable change in the genome or geneticinformation of a test subject with respect to a reference subject freeof the genetic variation. The presence or absence of a genetic variationcan be determined by analyzing and/or manipulating sequence reads thathave been mapped to genomic sections (e.g., genomic bins) as describedherein.

Counting

Sequence reads that have been mapped or partitioned based on a selectedfeature or variable can be quantified to determine the number of readsthat were mapped to each genomic section (e.g., bin, partition, genomicsegment and the like), in some embodiments. In certain embodiments, thetotal number of mapped sequence reads is determined by counting allmapped sequence reads, and in some embodiments the total number ofmapped sequence reads is determined by summing counts mapped to each binor partition. In certain embodiments, a subset of mapped sequence readsis determined by counting a predetermined subset of mapped sequencereads, and in some embodiments a predetermined subset of mapped sequencereads is determined by summing counts mapped to each predetermined binor partition. In some embodiments, predetermined subsets of mappedsequence reads can include from 1 to n-1 sequence reads, where nrepresents a number equal to the sum of all sequence reads generatedfrom a test subject or reference subject sample. In certain embodiments,predetermined subsets of mapped sequence reads can be selected utilizingany suitable feature or variable.

Quantifying or counting sequence reads can be done in any suitablemanner including but not limited to manual counting methods andautomated counting methods. In some embodiments, an automated countingmethod can be embodied in software that determines or counts the numberof sequence reads or sequence tags mapping to each chromosome and/or oneor more selected genomic sections. As used herein, software refers tocomputer readable program instructions that, when executed by acomputer, perform computer operations.

The number of sequence reads mapped to each bin and the total number ofsequence reads for samples derived from test subject and/or referencesubjects can be further analyzed and processed to provide an outcomedeterminative of the presence or absence of a genetic variation. Mappedsequence reads that have been counted sometimes are referred to as“data” or “data sets”. In some embodiments, data or data sets can becharacterized by one or more features or variables (e.g., sequence based[e.g., GC content, specific nucleotide sequence, the like], functionspecific [e.g., expressed genes, cancer genes, the like], location based[genome specific, chromosome specific, genomic section or bin specific],the like and combinations thereof). In certain embodiments, data or datasets can be organized into a matrix having two or more dimensions basedon one or more features of variables. Data organized into matrices canbe stratified using any suitable features or variables. A non-limitingexample of data organized into a matrix includes data that is stratifiedby maternal age, maternal ploidy, and fetal contribution. In certainembodiments, data sets characterized by one or more features orvariables sometimes are processed after counting.

Data Processing

Mapped sequence reads that have been counted are referred to herein asraw data, since the data represent unmanipulated counts (e.g., rawcounts). In some embodiments, sequence read data in a data set can beprocessed further (e.g., mathematically and/or statisticallymanipulated) and/or displayed to facilitate providing an outcome. Incertain embodiments, data sets, including larger data sets, may benefitfrom pre-processing to facilitate further analysis. Pre-processing ofdata sets sometimes involves removal of redundant and/or uninformativegenomic sections or bins (e.g., bins with uninformative data, redundantmapped reads, genomic sections or bins with zero median counts, overrepresented or under represented sequences). Without being limited bytheory, data processing and/or preprocessing may (i) remove noisy data,(ii) remove uninformative data, (iii) remove redundant data, (iv) reducethe complexity of larger data sets, and/or (v) facilitate transformationof the data from one form into one or more other forms. The terms“pre-processing” and “processing” when utilized with respect to data ordata sets are collectively referred to herein as “processing”.Processing can render data more amenable to further analysis, and cangenerate an outcome in some embodiments.

The term “noisy data” as used herein refers to (a) data that has asignificant variance between data points when analyzed or plotted, (b)data that has a significant standard deviation, (c) data that has asignificant standard error of the mean, the like, and combinations ofthe foregoing. Noisy data sometimes occurs due to the quantity and/orquality of starting material (e.g., nucleic acid sample), and sometimesoccurs as part of processes for preparing or replicating DNA used togenerate sequence reads. In certain embodiments, noise results fromcertain sequences being over represented when prepared using PCR-basedmethods. Methods described herein can reduce or eliminate thecontribution of noisy data, and therefore reduce the effect of noisydata on the provided outcome.

The terms “uninformative data”, “uninformative bins”, and “uninformativegenomic sections” as used herein refer to genomic sections, or dataderived therefrom, having a numerical value that is significantlydifferent from a predetermined cutoff threshold value or falls outside apredetermined cutoff range of values. A cutoff threshold value or rangeof values often is calculated by mathematically and/or statisticallymanipulating sequence read data (e.g., from a reference and/or subject),in some embodiments, and in certain embodiments, sequence read datamanipulated to generate a threshold cutoff value or range of values issequence read data (e.g., from a reference and/or subject). In someembodiments, a threshold cutoff value is obtained by calculating thestandard deviation and/or median absolute deviation (e.g., MAD) of a rawor normalized count profile and multiplying the standard deviation forthe profile by a constant representing the number of standard deviationschosen as a cutoff threshold (e.g., multiply by 3 for 3 standarddeviations), whereby a value for an uncertainty is generated. In certainembodiments, a portion or all of the genomic sections exceeding thecalculated uncertainty threshold cutoff value, or outside the range ofthreshold cutoff values, are removed as part of, prior to, or after thenormalization process. In some embodiments, a portion or all of thegenomic sections exceeding the calculated uncertainty threshold cutoffvalue, or outside the range of threshold cutoff values or raw datapoints, are weighted as part of, or prior to the normalization orclassification process. Examples of weighting are described herein. Theterms “redundant data”, and “redundant mapped reads” as used hereinrefer to sample derived sequences reads that are identified as havingalready been assigned to a genomic location (e.g., base position) and/orcounted for a genomic section.

Any suitable procedure can be utilized for processing data setsdescribed herein. Non-limiting examples of procedures suitable for usefor processing data sets include filtering, normalizing, weighting,monitoring peak heights, monitoring peak areas, monitoring peak edges,determining area ratios, mathematical processing of data, statisticalprocessing of data, application of statistical algorithms, analysis withfixed variables, analysis with optimized variables, plotting data toidentify patterns or trends for additional processing, the like andcombinations of the foregoing. In some embodiments, data sets areprocessed based on various features (e.g., GC content, redundant mappedreads, centromere regions, telomere regions, the like and combinationsthereof) and/or variables (e.g., fetal gender, maternal age, maternalploidy, percent contribution of fetal nucleic acid, the like orcombinations thereof). In certain embodiments, processing data sets asdescribed herein can reduce the complexity and/or dimensionality oflarge and/or complex data sets. A non-limiting example of a complex dataset includes sequence read data generated from one or more test subjectsand a plurality of reference subjects of different ages and ethnicbackgrounds. In some embodiments, data sets can include from thousandsto millions of sequence reads for each test and/or reference subject.

Data processing can be performed in any number of steps, in certainembodiments. For example, data may be processed using only a singleprocessing procedure in some embodiments, and in certain embodimentsdata may be processed using 1 or more, 5 or more, 10 or more or 20 ormore processing steps (e.g., 1 or more processing steps, 2 or moreprocessing steps, 3 or more processing steps, 4 or more processingsteps, 5 or more processing steps, 6 or more processing steps, 7 or moreprocessing steps, 8 or more processing steps, 9 or more processingsteps, 10 or more processing steps, 11 or more processing steps, 12 ormore processing steps, 13 or more processing steps, 14 or moreprocessing steps, 15 or more processing steps, 16 or more processingsteps, 17 or more processing steps, 18 or more processing steps, 19 ormore processing steps, or 20 or more processing steps). In someembodiments, processing steps may be the same step repeated two or moretimes (e.g., filtering two or more times, normalizing two or moretimes), and in certain embodiments, processing steps may be two or moredifferent processing steps (e.g., filtering, normalizing; normalizing,monitoring peak heights and edges; filtering, normalizing, normalizingto a reference, statistical manipulation to determine p-values, and thelike), carried out simultaneously or sequentially. In some embodiments,any suitable number and/or combination of the same or differentprocessing steps can be utilized to process sequence read data tofacilitate providing an outcome. In certain embodiments, processing datasets by the criteria described herein may reduce the complexity and/ordimensionality of a data set. In some embodiments, one or moreprocessing steps can comprise one or more filtering steps.

The term “filtering” as used herein refers to removing genomic sectionsor bins from consideration. Bins can be selected for removal based onany suitable criteria, including but not limited to redundant data(e.g., redundant or overlapping mapped reads), non-informative data(e.g., bins with zero median counts), bins with over represented orunder represented sequences, noisy data, the like, or combinations ofthe foregoing. A filtering process often involves removing one or morebins from consideration and subtracting the counts in the one or morebins selected for removal from the counted or summed counts for thebins, chromosome or chromosomes, or genome under consideration. In someembodiments, bins can be removed successively (e.g., one at a time toallow evaluation of the effect of removal of each individual bin), andin certain embodiments all bins marked for removal can be removed at thesame time.

In some embodiments, one or more processing steps can comprise one ormore normalization steps. The term “normalization” as used herein refersto division of one or more data sets by a predetermined variable. Anysuitable number of normalizations can be used. In some embodiments, datasets can be normalized 1 or more, 5 or more, 10 or more or even 20 ormore times. Data sets can be normalized to values (e.g., normalizingvalue) representative of any suitable feature or variable (e.g., sampledata, reference data, or both). Non-limiting examples of types of datanormalizations that can be used include normalizing raw count data forone or more selected test or reference genomic sections to the totalnumber of counts mapped to the chromosome or the entire genome on whichthe selected genomic section or sections are mapped; normalizing rawcount data for one or more selected genomic segments to a medianreference count for one or more genomic sections or the chromosome onwhich a selected genomic segment or segments is mapped; normalizing rawcount data to previously normalized data or derivatives thereof; andnormalizing previously normalized data to one or more otherpredetermined normalization variables. Normalizing a data set sometimeshas the effect of isolating statistical error, depending on the featureor property selected as the predetermined normalization variable.Normalizing a data set sometimes also allows comparison of datacharacteristics of data having different scales, by bringing the data toa common scale (e.g., predetermined normalization variable). In someembodiments, one or more normalizations to a statistically derived valuecan be utilized to minimize data differences and diminish the importanceof outlying data.

In some embodiments, a processing step comprises a weighting. The terms“weighted”, “weighting” or “weight function” or grammatical derivativesor equivalents thereof, as used herein, refer to a mathematicalmanipulation of a portion or all of a data set sometimes utilized toalter the influence of certain data set features or variables withrespect to other data set features or variables (e.g., increase ordecrease the significance and/or contribution of data contained in oneor more genomic sections or bins, based on the quality or usefulness ofthe data in the selected bin or bins). A weighting function can be usedto increase the influence of data with a relatively small measurementvariance, and/or to decrease the influence of data with a relativelylarge measurement variance, in some embodiments. For example, bins withunder represented or low quality sequence data can be “down weighted” tominimize the influence on a data set, whereas selected bins can be “upweighted” to increase the influence on a data set. A non-limitingexample of a weighting function is [1/(standard deviation)²]. Aweighting step sometimes is performed in a manner substantially similarto a normalizing step. In some embodiments, a data set is divided by apredetermined variable (e.g., weighting variable). A predeterminedvariable (e.g., minimized target function, Phi) often is selected toweigh different parts of a data set differently (e.g., increase theinfluence of certain data types while decreasing the influence of otherdata types).

In certain embodiments, a processing step can comprise one or moremathematical and/or statistical manipulations. Any suitable mathematicaland/or statistical manipulation, alone or in combination, may be used toanalyze and/or manipulate a data set described herein. Any suitablenumber of mathematical and/or statistical manipulations can be used. Insome embodiments, a data set can be mathematically and/or statisticallymanipulated 1 or more, 5 or more, 10 or more or 20 or more times.Non-limiting examples of mathematical and statistical manipulations thatcan be used include addition, subtraction, multiplication, division,algebraic functions, least squares estimators, curve fitting,differential equations, rational polynomials, double polynomials,orthogonal polynomials, z-scores, p-values, chi values, phi values,analysis of peak elevations, determination of peak edge locations,calculation of peak area ratios, analysis of median chromosomalelevation, calculation of mean absolute deviation, sum of squaredresiduals, mean, standard deviation, standard error, the like orcombinations thereof. A mathematical and/or statistical manipulation canbe performed on all or a portion of sequence read data, or processedproducts thereof. Non-limiting examples of data set variables orfeatures that can be statistically manipulated include raw counts,filtered counts, normalized counts, peak heights, peak widths, peakareas, peak edges, lateral tolerances, P-values, median elevations, meanelevations, count distribution within a genomic region, relativerepresentation of nucleic acid species, the like or combinationsthereof.

In some embodiments, a processing step can include the use of one ormore statistical algorithms. Any suitable statistical algorithm, aloneor in combination, may be used to analyze and/or manipulate a data setdescribed herein. Any suitable number of statistical algorithms can beused. In some embodiments, a data set can be analyzed using 1 or more, 5or more, 10 or more or 20 or more statistical algorithms. Non-limitingexamples of statistical algorithms suitable for use with methodsdescribed herein include decision trees, counternulls, multiplecomparisons, omnibus test, Behrens-Fisher problem, bootstrapping,Fisher's method for combining independent tests of significance, nullhypothesis, type I error, type II error, exact test, one-sample Z test,two-sample Z test, one-sample t-test, paired t-test, two-sample pooledt-test having equal variances, two-sample unpooled t-test having unequalvariances, one-proportion z-test, two-proportion z-test pooled,two-proportion z-test unpooled, one-sample chi-square test, two-sample Ftest for equality of variances, confidence interval, credible interval,significance, meta analysis, simple linear regression, robust linearregression, the like or combinations of the foregoing. Non-limitingexamples of data set variables or features that can be analyzed usingstatistical algorithms include raw counts, filtered counts, normalizedcounts, peak heights, peak widths, peak edges, lateral tolerances,P-values, median elevations, mean elevations, count distribution withina genomic region, relative representation of nucleic acid species, thelike or combinations thereof.

In certain embodiments, a data set can be analyzed by utilizing multiple(e.g., 2 or more) statistical algorithms (e.g., least squaresregression, principle component analysis, linear discriminant analysis,quadratic discriminant analysis, bagging, neural networks, supportvector machine models, random forests, classification tree models,K-nearest neighbors, logistic regression and/or loss smoothing) and/ormathematical and/or statistical manipulations (e.g., referred to hereinas manipulations). The use of multiple manipulations can generate anN-dimensional space that can be used to provide an outcome, in someembodiments. In certain embodiments, analysis of a data set by utilizingmultiple manipulations can reduce the complexity and/or dimensionalityof the data set. For example, the use of multiple manipulations on areference data set can generate an N-dimensional space (e.g.,probability plot) that can be used to represent the presence or absenceof a genetic variation, depending on the genetic status of the referencesamples (e.g., positive or negative for a selected genetic variation).Analysis of test samples using a substantially similar set ofmanipulations can be used to generate an N-dimensional point for each ofthe test samples. The complexity and/or dimensionality of a test subjectdata set sometimes is reduced to a single value or N-dimensional pointthat can be readily compared to the N-dimensional space generated fromthe reference data. Test sample data that fall within the N-dimensionalspace populated by the reference subject data are indicative of agenetic status substantially similar to that of the reference subjects.Test sample data that fall outside of the N-dimensional space populatedby the reference subject data are indicative of a genetic statussubstantially dissimilar to that of the reference subjects. In someembodiments, references are euploid or do not otherwise have a geneticvariation or medical condition.

In some embodiments, a processing step can comprise generating one ormore profiles (e.g., profile plot) from various aspects of a data set orderivation thereof (e.g., product of one or more mathematical and/orstatistical data processing steps known in the art and/or describedherein). The term “profile” as used herein refers to mathematical and/orstatistical manipulation of data that facilitates identification ofpatterns and/or correlations in large quantities of data. Thus, the term“profile” as used herein often refers to values resulting from one ormore manipulations of data or data sets, based on one or more criteria.A profile often includes multiple data points. Any suitable number ofdata points may be included in a profile depending on the nature and/orcomplexity of a data set. In certain embodiments, profiles may include 2or more data points, 3 or more data points, 5 or more data points, 10 ormore data points, 24 or more data points, 25 or more data points, 50 ormore data points, 100 or more data points, 500 or more data points, 1000or more data points, 5000 or more data points, 10,000 or more datapoints, or 100,000 or more data points.

In some embodiments, a profile is representative of the entirety of adata set, and in certain embodiments, a profile is representative of aportion or subset of a data set. That is, a profile sometimes includesor is generated from data points representative of data that has notbeen filtered to remove any data, and sometimes a profile includes or isgenerated from data points representative of data that has been filteredto remove unwanted data. In some embodiments, a data point in a profilerepresents the results of data manipulation for a genomic section. Incertain embodiments, a data point in a profile represents the results ofdata manipulation for groups of genomic sections. In some embodiments,groups of genomic sections may be adjacent to one another, and incertain embodiments, groups of genomic sections may be from differentparts of a chromosome or genome.

Data points in a profile derived from a data set can be representativeof any suitable data categorization. Non-limiting examples of categoriesinto which data can be grouped to generate profile data points include:genomic sections based on sized, genomic sections based on sequencefeatures (e.g., GC content, AT content, position on a chromosome (e.g.,short arm, long arm, centromere, telomere), and the like), levels ofexpression, chromosome, the like or combinations thereof. In someembodiments, a profile may be generated from data points obtained fromanother profile (e.g., normalized data profile renormalized to adifferent normalizing value to generate a renormalized data profile). Incertain embodiments, a profile generated from data points obtained fromanother profile reduces the number of data points and/or complexity ofthe data set. Reducing the number of data points and/or complexity of adata set often facilitates interpretation of data and/or facilitatesproviding an outcome.

A profile frequently is presented as a plot, and non-limiting examplesof profile plots that can be generated include raw count (e.g., rawcount profile or raw profile), normalized count (e.g., normalized countprofile or normalized profile), bin-weighted, z-score, p-value, arearatio versus fitted ploidy, median elevation versus ratio between fittedand measured fetal fraction, principle components, the like, orcombinations thereof. Profile plots allow visualization of themanipulated data, in some embodiments. In certain embodiments, a profileplot can be utilized to provide an outcome (e.g., area ratio versusfitted ploidy, median elevation versus ratio between fitted and measuredfetal fraction, principle components). The terms “raw count profileplot” or “raw profile plot” as used herein refer to a plot of counts ineach genomic section in a region normalized to total counts in a region(e.g., genome, chromosome, portion of chromosome).

A profile generated for a test subject sometimes is compared to aprofile generated for one or more reference subjects, to facilitateinterpretation of mathematical and/or statistical manipulations of adata set and/or to provide an outcome. In some embodiments, a profile isgenerated based on one or more starting assumptions (e.g., maternalcontribution of nucleic acid (e.g., maternal fraction), fetalcontribution of nucleic acid (e.g., fetal fraction), ploidy of referencesample, the like or combinations thereof). In certain embodiments, atest profile often centers around a predetermined value representativeof the absence of a genetic variation, and often deviates from apredetermined value in areas corresponding to the genomic location inwhich the genetic variation is located in the test subject, if the testsubject possessed the genetic variation. In test subjects at risk for,or suffering from a medical condition associated with a geneticvariation, the numerical value for a selected genomic section isexpected to vary significantly from the predetermined value fornon-affected genomic locations. Depending on starting assumptions (e.g.,fixed ploidy or optimized ploidy, fixed fetal fraction or optimizedfetal fraction or combinations thereof) the predetermined threshold orcutoff value or range of values indicative of the presence or absence ofa genetic variation can vary while still providing an outcome useful fordetermining the presence or absence of a genetic variation. In someembodiments, a profile is indicative of and/or representative of aphenotype.

By way of a non-limiting example, normalized sample and/or referencecount profiles can be obtained from raw sequence read data by (a)calculating reference median counts for selected chromosomes, genomicsections or portions thereof from a set of references known not to carrya genetic variation, (b) removal of uninformative genomic sections fromthe reference sample raw counts (e.g., filtering); (c) normalizing thereference counts for all remaining bins to the total residual number ofcounts (e.g., sum of remaining counts after removal of uninformativebins) for the reference sample selected chromosome or selected genomiclocation, thereby generating a normalized reference subject profile; (d)removing the corresponding genomic sections from the test subjectsample; and (e) normalizing the remaining test subject counts for one ormore selected genomic locations to the sum of the residual referencemedian counts for the chromosome or chromosomes containing the selectedgenomic locations, thereby generating a normalized test subject profile.In certain embodiments, an additional normalizing step with respect tothe entire genome, reduced by the filtered genomic sections in (b), canbe included between (c) and (d).

In some embodiments, the use of one or more reference samples known tobe free of a genetic variation in question can be used to generate areference median count profile, which may result in a predeterminedvalue representative of the absence of the genetic variation, and oftendeviates from a predetermined value in areas corresponding to thegenomic location in which the genetic variation is located in the testsubject, if the test subject possessed the genetic variation. In testsubjects at risk for, or suffering from a medical condition associatedwith a genetic variation, the numerical value for the selected genomicsection or sections is expected to vary significantly from thepredetermined value for non-affected genomic locations. In certainembodiments, the use of one or more reference samples known to carry thegenetic variation in question can be used to generate a reference mediancount profile, which may result in a predetermined value representativeof the presence of the genetic variation, and often deviates from apredetermined value in areas corresponding to the genomic location inwhich a test subject does not carry the genetic variation. In testsubjects not at risk for, or suffering from a medical conditionassociated with a genetic variation, the numerical value for theselected genomic section or sections is expected to vary significantlyfrom the predetermined value for affected genomic locations.

In some embodiments, analysis and processing of data can include the useof one or more assumptions. Any suitable number or type of assumptionscan be utilized to analyze or process a data set. Non-limiting examplesof assumptions that can be used for data processing and/or analysisinclude maternal ploidy, fetal contribution, prevalence of certainsequences in a reference population, ethnic background, prevalence of aselected medical condition in related family members, parallelismbetween raw count profiles from different patients and/or runs afterGC-normalization and repeat masking (e.g., GCRM), identical matchesrepresent PCR artifacts (e.g., identical base position), assumptionsinherent in a fetal quantifier assay (e.g., FQA), assumptions regardingtwins (e.g., if 2 twins and only 1 is affected the effective fetalfraction is only 50% of the total measured fetal fraction (similarly fortriplets, quadruplets and the like)), fetal cell free DNA (e.g., cfDNA)uniformly covers the entire genome, the like and combinations thereof.

In those instances where the quality and/or depth of mapped sequencereads does not permit an outcome prediction of the presence or absenceof a genetic variation at a desired confidence level (e.g., 95% orhigher confidence level), based on the normalized count profiles, one ormore additional mathematical manipulation algorithms and/or statisticalprediction algorithms, can be utilized to generate additional numericalvalues useful for data analysis and/or providing an outcome. The term“normalized count profile” as used herein refers to a profile generatedusing normalized counts. Examples of methods that can be used togenerate normalized counts and normalized count profiles are describedherein. As noted, mapped sequence reads that have been counted can benormalized with respect to test sample counts or reference samplecounts. In some embodiments, a normalized count profile can be presentedas a plot.

As noted above, data sometimes is transformed from one form into anotherform. The terms “transformed”, “transformation”, and grammaticalderivations or equivalents thereof, as used herein refer to analteration of data from a physical starting material (e.g., test subjectand/or reference subject sample nucleic acid) into a digitalrepresentation of the physical starting material (e.g., sequence readdata), and in some embodiments includes a further transformation intoone or more numerical values or graphical representations of the digitalrepresentation that can be utilized to provide an outcome. In certainembodiments, the one or more numerical values and/or graphicalrepresentations of digitally represented data can be utilized torepresent the appearance of a test subject's physical genome (e.g.,virtually represent or visually represent the presence or absence of agenomic insertion or genomic deletion; represent the presence or absenceof a variation in the physical amount of a sequence associated withmedical conditions). A virtual representation sometimes is furthertransformed into one or more numerical values or graphicalrepresentations of the digital representation of the starting material.These procedures can transform physical starting material into anumerical value or graphical representation, or a representation of thephysical appearance of a test subject's genome.

In some embodiments, transformation of a data set facilitates providingan outcome by reducing data complexity and/or data dimensionality. Dataset complexity sometimes is reduced during the process of transforming aphysical starting material into a virtual representation of the startingmaterial (e.g., sequence reads representative of physical startingmaterial). Any suitable feature or variable can be utilized to reducedata set complexity and/or dimensionality. Non-limiting examples offeatures that can be chosen for use as a target feature for dataprocessing include GC content, fetal gender prediction, identificationof chromosomal aneuploidy, identification of particular genes orproteins, identification of cancer, diseases, inherited genes/traits,chromosomal abnormalities, a biological category, a chemical category, abiochemical category, a category of genes or proteins, a gene ontology,a protein ontology, co-regulated genes, cell signaling genes, cell cyclegenes, proteins pertaining to the foregoing genes, gene variants,protein variants, co-regulated genes, co-regulated proteins, amino acidsequence, nucleotide sequence, protein structure data and the like, andcombinations of the foregoing. Non-limiting examples of data setcomplexity and/or dimensionality reduction include; reduction of aplurality of sequence reads to profile plots, reduction of a pluralityof sequence reads to numerical values (e.g., normalized values,Z-scores, p-values); reduction of multiple analysis methods toprobability plots or single points; principle component analysis ofderived quantities; and the like or combinations thereof.

Outcome

Analysis and processing of data can provide one or more outcomes. Theterm “outcome” as used herein refers to a result of data processing thatfacilitates determining whether a subject was, or is at risk of having,a genetic variation. An outcome often comprises one or more numericalvalues generated using a processing method described herein in thecontext of one or more considerations of probability. A consideration ofprobability includes but is not limited to: measure of variability,confidence level, sensitivity, specificity, standard deviation,coefficient of variation (CV) and/or confidence level, Z-scores, Chivalues, Phi values, ploidy values, fitted fetal fraction, area ratios,median elevation, the like or combinations thereof. A consideration ofprobability can facilitate determining whether a subject is at risk ofhaving, or has, a genetic variation, and an outcome determinative of apresence or absence of a genetic disorder often includes such aconsideration.

An outcome often is a phenotype with an associated level of confidence(e.g., fetus is positive for trisomy 21 with a confidence level of 99%,test subject is negative for a cancer associated with a geneticvariation at a confidence level of 95%). Different methods of generatingoutcome values sometimes can produce different types of results.Generally, there are four types of possible scores or calls that can bemade based on outcome values generated using methods described herein:true positive, false positive, true negative and false negative. Theterms “score”, “scores”, “call” and “calls” as used herein refer tocalculating the probability that a particular genetic variation ispresent or absent in a subject/sample. The value of a score may be usedto determine, for example, a variation, difference, or ratio of mappedsequence reads that may correspond to a genetic variation. For example,calculating a positive score for a selected genetic variation or genomicsection from a data set, with respect to a reference genome can lead toan identification of the presence or absence of a genetic variation,which genetic variation sometimes is associated with a medical condition(e.g., cancer, preeclampsia, trisomy, monosomy, and the like). In someembodiments, an outcome comprises a profile. In those embodiments inwhich an outcome comprises a profile, any suitable profile orcombination of profiles can be used for an outcome. Non-limitingexamples of profiles that can be used for an outcome include z-scoreprofiles, p-value profiles, chi value profiles, phi value profiles, thelike, and combinations thereof

An outcome generated for determining the presence or absence of agenetic variation sometimes includes a null result (e.g., a data pointbetween two clusters, a numerical value with a standard deviation thatencompasses values for both the presence and absence of a geneticvariation, a data set with a profile plot that is not similar to profileplots for subjects having or free from the genetic variation beinginvestigated). In some embodiments, an outcome indicative of a nullresult still is a determinative result, and the determination caninclude the need for additional information and/or a repeat of the datageneration and/or analysis for determining the presence or absence of agenetic variation.

An outcome can be generated after performing one or more processingsteps described herein, in some embodiments. In certain embodiments, anoutcome is generated as a result of one of the processing stepsdescribed herein, and in some embodiments, an outcome can be generatedafter each statistical and/or mathematical manipulation of a data set isperformed. An outcome pertaining to the determination of the presence orabsence of a genetic variation can be expressed in any suitable form,which form comprises without limitation, a probability (e.g., oddsratio, p-value), likelihood, value in or out of a cluster, value over orunder a threshold value, value with a measure of variance or confidence,or risk factor, associated with the presence or absence of a geneticvariation for a subject or sample. In certain embodiments, comparisonbetween samples allows confirmation of sample identity (e.g., allowsidentification of repeated samples and/or samples that have been mixedup (e.g., mislabeled, combined, and the like)).

In some embodiments, an outcome comprises a value above or below apredetermined threshold or cutoff value (e.g., greater than 1, less than1), and an uncertainty or confidence level associated with the value. Anoutcome also can describe any assumptions used in data processing. Incertain embodiments, an outcome comprises a value that falls within oroutside a predetermined range of values and the associated uncertaintyor confidence level for that value being inside or outside the range. Insome embodiments, an outcome comprises a value that is equal to apredetermined value (e.g., equal to 1, equal to zero), or is equal to avalue within a predetermined value range, and its associated uncertaintyor confidence level for that value being equal or within or outside arange. An outcome sometimes is graphically represented as a plot (e.g.,profile plot).

As noted above, an outcome can be characterized as a true positive, truenegative, false positive or false negative. The term “true positive” asused herein refers to a subject correctly diagnosed as having a geneticvariation. The term “false positive” as used herein refers to a subjectwrongly identified as having a genetic variation. The term “truenegative” as used herein refers to a subject correctly identified as nothaving a genetic variation. The term “false negative” as used hereinrefers to a subject wrongly identified as not having a geneticvariation. Two measures of performance for any given method can becalculated based on the ratios of these occurrences: (i) a sensitivityvalue, which generally is the fraction of predicted positives that arecorrectly identified as being positives; and (ii) a specificity value,which generally is the fraction of predicted negatives correctlyidentified as being negative. The term “sensitivity” as used hereinrefers to the number of true positives divided by the number of truepositives plus the number of false negatives, where sensitivity (sens)may be within the range of 0≦sens≦1. Ideally, the number of falsenegatives equal zero or close to zero, so that no subject is wronglyidentified as not having at least one genetic variation when they indeedhave at least one genetic variation. Conversely, an assessment often ismade of the ability of a prediction algorithm to classify negativescorrectly, a complementary measurement to sensitivity. The term“specificity” as used herein refers to the number of true negativesdivided by the number of true negatives plus the number of falsepositives, where sensitivity (spec) may be within the range of 0≦spec≦1.Ideally, the number of false positives equal zero or close to zero, sothat no subject is wrongly identified as having at least one geneticvariation when they do not have the genetic variation being assessed.

In certain embodiments, one or more of sensitivity, specificity and/orconfidence level are expressed as a percentage. In some embodiments, thepercentage, independently for each variable, is greater than about 90%(e.g., about 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99%, or greater than99% (e.g., about 99.5%, or greater, about 99.9% or greater, about 99.95%or greater, about 99.99% or greater)). Coefficient of variation (CV) insome embodiments is expressed as a percentage, and sometimes thepercentage is about 10% or less (e.g., about 10, 9, 8, 7, 6, 5, 4, 3, 2or 1%, or less than 1% (e.g., about 0.5% or less, about 0.1% or less,about 0.05% or less, about 0.01% or less)). A probability (e.g., that aparticular outcome is not due to chance) in certain embodiments isexpressed as a Z-score, a p-value, or the results of a t-test. In someembodiments, a measured variance, confidence interval, sensitivity,specificity and the like (e.g., referred to collectively as confidenceparameters) for an outcome can be generated using one or more dataprocessing manipulations described herein.

A method that has sensitivity and specificity equaling one, or 100%, ornear one (e.g., between about 90% to about 99%) sometimes is selected.In some embodiments, a method having a sensitivity equaling 1, or 100%is selected, and in certain embodiments, a method having a sensitivitynear 1 is selected (e.g., a sensitivity of about 90%, a sensitivity ofabout 91%, a sensitivity of about 92%, a sensitivity of about 93%, asensitivity of about 94%, a sensitivity of about 95%, a sensitivity ofabout 96%, a sensitivity of about 97%, a sensitivity of about 98%, or asensitivity of about 99%). In some embodiments, a method having aspecificity equaling 1, or 100% is selected, and in certain embodiments,a method having a specificity near 1 is selected (e.g., a specificity ofabout 90%, a specificity of about 91%, a specificity of about 92%, aspecificity of about 93%, a specificity of about 94%, a specificity ofabout 95%, a specificity of about 96%, a specificity of about 97%, aspecificity of about 98%, or a specificity of about 99%).

After one or more outcomes have been generated, an outcome often is usedto provide a determination of the presence or absence of a geneticvariation and/or associated medical condition. An outcome typically isprovided to a health care professional (e.g., laboratory technician ormanager; physician or assistant). In some embodiments, an outcomedeterminative of the presence or absence of a genetic variation isprovided to a healthcare professional in the form of a report, and incertain embodiments the report comprises a display of an outcome valueand an associated confidence parameter. Generally, an outcome can bedisplayed in any suitable format that facilitates determination of thepresence or absence of a genetic variation and/or medical condition.Non-limiting examples of formats suitable for use for reporting and/ordisplaying data sets or reporting an outcome include digital data, agraph, a 2D graph, a 3D graph, and 4D graph, a picture, a pictograph, achart, a bar graph, a pie graph, a diagram, a flow chart, a scatterplot, a map, a histogram, a density chart, a function graph, a circuitdiagram, a block diagram, a bubble map, a constellation diagram, acontour diagram, a cartogram, spider chart, Venn diagram, nomogram, andthe like, and combination of the foregoing.

Use of Outcomes

A health care professional, or other qualified individual, receiving areport comprising one or more outcomes determinative of the presence orabsence of a genetic variation can use the displayed data in the reportto make a call regarding the status of the test subject or patient. Thehealthcare professional can make a recommendation based on the providedoutcome, in some embodiments. A health care professional or qualifiedindividual can provide a test subject or patient with a call or scorewith regards to the presence or absence of the genetic variation basedon the outcome value or values and associated confidence parametersprovided in a report, in some embodiments. In certain embodiments, ascore or call is made manually by a healthcare professional or qualifiedindividual, using visual observation of the provided report. In certainembodiments, a score or call is made by an automated routine, sometimesembedded in software, and reviewed by a healthcare professional orqualified individual for accuracy prior to providing information to atest subject or patient. The term “receiving a report” as used hereinrefers to obtaining, by any communication means, a written and/orgraphical representation comprising an outcome, which upon review allowsa healthcare professional or other qualified individual to make adetermination as to the presence or absence of a genetic variation in atest subject or patient. The report may be generated by a computer or byhuman data entry, and can be communicated using electronic means (e.g.,over the internet, via computer, via fax, from one network location toanother location at the same or different physical sites), or by anyother method of sending or receiving data (e.g., mail service, courierservice and the like). In some embodiments the outcome is transmitted toa health care professional in a suitable medium, including, withoutlimitation, in verbal, document, or file form. The file may be, forexample, but not limited to, an auditory file, a computer readable file,a paper file, a laboratory file or a medical record file.

The term “providing an outcome” and grammatical equivalents thereof, asused herein also can refer to any method for obtaining such information,including, without limitation, obtaining the information from alaboratory file. A laboratory file can be generated by a laboratory thatcarried out one or more assays or one or more data processing steps todetermine the presence or absence of the medical condition. Thelaboratory may be in the same location or different location (e.g., inanother country) as the personnel identifying the presence or absence ofthe medical condition from the laboratory file. For example, thelaboratory file can be generated in one location and transmitted toanother location in which the information therein will be transmitted tothe pregnant female subject. The laboratory file may be in tangible formor electronic form (e.g., computer readable form), in certainembodiments.

A healthcare professional or qualified individual, can provide anysuitable recommendation based on the outcome or outcomes provided in thereport. Non-limiting examples of recommendations that can be providedbased on the provided outcome report includes, surgery, radiationtherapy, chemotherapy, genetic counseling, after birth treatmentsolutions (e.g., life planning, long term assisted care, medicaments,symptomatic treatments), pregnancy termination, organ transplant, bloodtransfusion, the like or combinations of the foregoing. In someembodiments the recommendation is dependent on the outcome basedclassification provided (e.g., Down's syndrome, Turner syndrome, medicalconditions associated with genetic variations in T13, medical conditionsassociated with genetic variations in T18).

Software can be used to perform one or more steps in the processdescribed herein, including but not limited to; counting, dataprocessing, generating an outcome, and/or providing one or morerecommendations based on generated outcomes.

Machines, Software and Interfaces

Apparatuses, software and interfaces may be used to conduct methodsdescribed herein. Using apparatuses, software and interfaces, a user mayenter, request, query or determine options for using particularinformation, programs or processes (e.g., mapping sequence reads,processing mapped data and/or providing an outcome), which can involveimplementing statistical analysis algorithms, statistical significancealgorithms, statistical algorithms, iterative steps, validationalgorithms, and graphical representations, for example. In someembodiments, a data set may be entered by a user as input information, auser may download one or more data sets by any suitable hardware media(e.g., flash drive), and/or a user may send a data set from one systemto another for subsequent processing and/or providing an outcome (e.g.,send sequence read data from a sequencer to a computer system forsequence read mapping; send mapped sequence data to a computer systemfor processing and yielding an outcome and/or report).

A user may, for example, place a query to software which then mayacquire a data set via internet access, and in certain embodiments, aprogrammable processor may be prompted to acquire a suitable data setbased on given parameters. A programmable processor also may prompt auser to select one or more data set options selected by the processorbased on given parameters. A programmable processor may prompt a user toselect one or more data set options selected by the processor based oninformation found via the internet, other internal or externalinformation, or the like. Options may be chosen for selecting one ormore data feature selections, one or more statistical algorithms, one ormore statistical analysis algorithms, one or more statisticalsignificance algorithms, iterative steps, one or more validationalgorithms, and one or more graphical representations of methods,apparatuses, or computer programs.

Systems addressed herein may comprise general components of computersystems, such as, for example, network servers, laptop systems, desktopsystems, handheld systems, personal digital assistants, computingkiosks, and the like. A computer system may comprise one or more inputmeans such as a keyboard, touch screen, mouse, voice recognition orother means to allow the user to enter data into the system. A systemmay further comprise one or more outputs, including, but not limited to,a display screen (e.g., CRT or LCD), speaker, FAX machine, printer(e.g., laser, ink jet, impact, black and white or color printer), orother output useful for providing visual, auditory and/or hardcopyoutput of information (e.g., outcome and/or report).

In a system, input and output means may be connected to a centralprocessing unit which may comprise among other components, amicroprocessor for executing program instructions and memory for storingprogram code and data. In some embodiments, processes may be implementedas a single user system located in a single geographical site. Incertain embodiments, processes may be implemented as a multi-usersystem. In the case of a multi-user implementation, multiple centralprocessing units may be connected by means of a network. The network maybe local, encompassing a single department in one portion of a building,an entire building, span multiple buildings, span a region, span anentire country or be worldwide. The network may be private, being ownedand controlled by a provider, or it may be implemented as an internetbased service where the user accesses a web page to enter and retrieveinformation. Accordingly, in certain embodiments, a system includes oneor more machines, which may be local or remote with respect to a user.More than one machine in one location or multiple locations may beaccessed by a user, and data may be mapped and/or processed in seriesand/or in parallel. Thus, any suitable configuration and control may beutilized for mapping and/or processing data using multiple machines,such as in local network, remote network and/or “cloud” computingplatforms.

A system can include a communications interface in some embodiments. Acommunications interface allows for transfer of software and databetween a computer system and one or more external devices. Non-limitingexamples of communications interfaces include a modem, a networkinterface (such as an Ethernet card), a communications port, a PCMCIAslot and card, and the like. Software and data transferred via acommunications interface generally are in the form of signals, which canbe electronic, electromagnetic, optical and/or other signals capable ofbeing received by a communications interface. Signals often are providedto a communications interface via a channel. A channel often carriessignals and can be implemented using wire or cable, fiber optics, aphone line, a cellular phone link, an RF link and/or othercommunications channels. Thus, in an example, a communications interfacemay be used to receive signal information that can be detected by asignal detection module.

Data may be input by any suitable device and/or method, including, butnot limited to, manual input devices or direct data entry devices(DDEs). Non-limiting examples of manual devices include keyboards,concept keyboards, touch sensitive screens, light pens, mouse, trackerballs, joysticks, graphic tablets, scanners, digital cameras, videodigitizers and voice recognition devices. Non-limiting examples of DDEsinclude bar code readers, magnetic strip codes, smart cards, magneticink character recognition, optical character recognition, optical markrecognition, and turnaround documents.

In some embodiments, output from a sequencing apparatus may serve asdata that can be input via an input device. In certain embodiments,mapped sequence reads may serve as data that can be input via an inputdevice. In certain embodiments, simulated data is generated by an insilico process and the simulated data serves as data that can be inputvia an input device. The term “in silico” refers to research andexperiments performed using a computer. In silico processes include, butare not limited to, mapping sequence reads and processing mappedsequence reads according to processes described herein.

A system may include software useful for performing a process describedherein, and software can include one or more modules for performing suchprocesses (e.g., data acquisition module, data processing module, datadisplay module). The term “software” refers to computer readable programinstructions that, when executed by a computer, perform computeroperations. The term “module” refers to a self-contained functional unitthat can be used in a larger software system. For example, a softwaremodule is a part of a program that performs a particular process ortask.

Software often is provided on a program product containing programinstructions recorded on a computer readable medium, including, but notlimited to, magnetic media including floppy disks, hard disks, andmagnetic tape; and optical media including CD-ROM discs, DVD discs,magneto-optical discs, flash drives, RAM, floppy discs, the like, andother such media on which the program instructions can be recorded. Inonline implementation, a server and web site maintained by anorganization can be configured to provide software downloads to remoteusers, or remote users may access a remote system maintained by anorganization to remotely access software.

Software may obtain or receive input information. Software may include amodule that specifically obtains or receives data (e.g., a datareceiving module that receives sequence read data and/or mapped readdata) and may include a module that specifically processes the data(e.g., a processing module that processes received data (e.g., filters,normalizes, provides an outcome and/or report). The terms “obtaining”and “receiving” input information refers to receiving data (e.g.,sequence reads, mapped reads) by computer communication means from alocal, or remote site, human data entry, or any other method ofreceiving data. The input information may be generated in the samelocation at which it is received, or it may be generated in a differentlocation and transmitted to the receiving location. In some embodiments,input information is modified before it is processed (e.g., placed intoa format amenable to processing (e.g., tabulated)).

In some embodiments, provided are computer program products, such as,for example, a computer program product comprising a computer usablemedium having a computer readable program code embodied therein, thecomputer readable program code adapted to be executed to implement amethod comprising: (a) obtaining nucleotide sequence reads from a samplecomprising circulating, cell-free nucleic acid from a pregnant female,where the sample has been enriched for vesicle-free and/or a certainhistone-associated nucleic acid species, (b) mapping the nucleotidesequence reads to reference genome sections, (c) counting the number ofnucleotide sequence reads mapped to each reference genome section, (d)comparing the number of counts of the nucleotide sequence reads mappedin (c), or derivative thereof, to a reference, or portion thereof,thereby making a comparison, and (e) providing an outcome determinativeof the presence or absence of a fetal aneuploidy based on thecomparison.

Software can include one or more algorithms in certain embodiments. Analgorithm may be used for processing data and/or providing an outcome orreport according to a finite sequence of instructions. An algorithmoften is a list of defined instructions for completing a task. Startingfrom an initial state, the instructions may describe a computation thatproceeds through a defined series of successive states, eventuallyterminating in a final ending state. The transition from one state tothe next is not necessarily deterministic (e.g., some algorithmsincorporate randomness). By way of example, and without limitation, analgorithm can be a search algorithm, sorting algorithm, merge algorithm,numerical algorithm, graph algorithm, string algorithm, modelingalgorithm, computational genometric algorithm, combinatorial algorithm,machine learning algorithm, cryptography algorithm, data compressionalgorithm, parsing algorithm and the like. An algorithm can include onealgorithm or two or more algorithms working in combination. An algorithmcan be of any suitable complexity class and/or parameterized complexity.An algorithm can be used for calculation and/or data processing, and insome embodiments, can be used in a deterministic orprobabilistic/predictive approach. An algorithm can be implemented in acomputing environment by use of a suitable programming language,non-limiting examples of which are C, C++, Java, Perl, Python, Fortran,and the like. In some embodiments, an algorithm can be configured ormodified to include margin of errors, statistical analysis, statisticalsignificance, and/or comparison to other information or data sets (e.g.,applicable when using a neural net or clustering algorithm).

In certain embodiments, several algorithms may be implemented for use insoftware. These algorithms can be trained with raw data in someembodiments. For each new raw data sample, the trained algorithms mayproduce a representative processed data set or outcome. A processed dataset sometimes is of reduced complexity compared to the parent data setthat was processed. Based on a processed set, the performance of atrained algorithm may be assessed based on sensitivity and specificity,in some embodiments. An algorithm with the highest sensitivity and/orspecificity may be identified and utilized, in certain embodiments.

In certain embodiments, simulated (or simulation) data can aid dataprocessing, for example, by training an algorithm or testing analgorithm. In some embodiments, simulated data includes hypotheticalvarious samplings of different groupings of sequence reads. Simulateddata may be based on what might be expected from a real population ormay be skewed to test an algorithm and/or to assign a correctclassification. Simulated data also is referred to herein as “virtual”data. Simulations can be performed by a computer program in certainembodiments. One possible step in using a simulated data set is toevaluate the confidence of an identified results, e.g., how well arandom sampling matches or best represents the original data. Oneapproach is to calculate a probability value (p-value), which estimatesthe probability of a random sample having better score than the selectedsamples. In some embodiments, an empirical model may be assessed, inwhich it is assumed that at least one sample matches a reference sample(with or without resolved variations). In some embodiments, anotherdistribution, such as a Poisson distribution for example, can be used todefine the probability distribution.

A system may include one or more processors in certain embodiments. Aprocessor can be connected to a communication bus. A computer system mayinclude a main memory, often random access memory (RAM), and can alsoinclude a secondary memory. Secondary memory can include, for example, ahard disk drive and/or a removable storage drive, representing a floppydisk drive, a magnetic tape drive, an optical disk drive, memory cardand the like. A removable storage drive often reads from and/or writesto a removable storage unit. Non-limiting examples of removable storageunits include a floppy disk, magnetic tape, optical disk, and the like,which can be read by and written to by, for example, a removable storagedrive. A removable storage unit can include a computer-usable storagemedium having stored therein computer software and/or data.

A processor may implement software in a system. In some embodiments, aprocessor may be programmed to automatically perform a task describedherein that a user could perform. Accordingly, a processor, or algorithmconducted by such a processor, can require little to no supervision orinput from a user (e.g., software may be programmed to implement afunction automatically). In some embodiments, the complexity of aprocess is so large that a single person or group of persons could notperform the process in a timeframe short enough for providing an outcomedeterminative of the presence or absence of a genetic variation.

In some embodiments, secondary memory may include other similar meansfor allowing computer programs or other instructions to be loaded into acomputer system. For example, a system can include a removable storageunit and an interface device. Non-limiting examples of such systemsinclude a program cartridge and cartridge interface (such as that foundin video game devices), a removable memory chip (such as an EPROM, orPROM) and associated socket, and other removable storage units andinterfaces that allow software and data to be transferred from theremovable storage unit to a computer system.

Genetic Variations and Medical Conditions

The presence or absence of a genetic variance can be determined using amethod or apparatus described herein. In certain embodiments, thepresence or absence of one or more genetic variations is determinedaccording to an outcome provided by methods and apparatuses describedherein. A genetic variation generally is a particular genetic phenotypepresent in certain individuals, and often a genetic variation is presentin a statistically significant sub-population of individuals. In someembodiments, a genetic variation is a chromosome abnormality (e.g.,aneuploidy), partial chromosome abnormality or mosaicism, each of whichis described in greater detail herein. Non-limiting examples of geneticvariations include one or more deletions (e.g., micro-deletions),duplications (e.g., micro-duplications), insertions, mutations,polymorphisms (e.g., single-nucleotide polymorphisms), fusions, repeats(e.g., short tandem repeats), distinct methylation sites, distinctmethylation patterns, the like and combinations thereof. An insertion,repeat, deletion, duplication, mutation or polymorphism can be of anylength, and in some embodiments, is about 1 base or base pair (bp) toabout 250 megabases (Mb) in length. In some embodiments, an insertion,repeat, deletion, duplication, mutation or polymorphism is about 1 baseor base pair (bp) to about 1,000 kilobases (kb) in length (e.g., about10 bp, 50 bp, 100 bp, 500 bp, 1 kb, 5 kb, 10 kb, 50 kb, 100 kb, 500 kb,or 1000 kb in length).

A genetic variation is sometime a deletion. In some embodiments, adeletion is a mutation (e.g., a genetic aberration) in which a part of achromosome or a sequence of DNA is missing. A deletion is often the lossof genetic material. Any number of nucleotides can be deleted. Adeletion can comprise the deletion of one or more entire chromosomes, asegment of a chromosome, an allele, a gene, an intron, an exon, anynon-coding region, any coding region, a segment thereof or combinationthereof. A deletion can comprise a microdeletion. A deletion cancomprise the deletion of a single base.

A genetic variation is sometimes a genetic duplication. In someembodiments, a duplication is a mutation (e.g., a genetic aberration) inwhich a part of a chromosome or a sequence of DNA is copied and insertedback into the genome. In some embodiments, a genetic duplication (i.e.duplication) is any duplication of a region of DNA. In some embodimentsa duplication is a nucleic acid sequence that is repeated, often intandem, within a genome or chromosome. In some embodiments a duplicationcan comprise a copy of one or more entire chromosomes, a segment of achromosome, an allele, a gene, an intron, an exon, any non-codingregion, any coding region, segment thereof or combination thereof. Aduplication can comprise a microduplication. A duplication sometimescomprises one or more copies of a duplicated nucleic acid. A duplicationsometimes is characterized as a genetic region repeated one or moretimes (e.g., repeated 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 times).Duplications can range from small regions (thousands of base pairs) towhole chromosomes in some instances. Duplications frequently occur asthe result of an error in homologous recombination or due to aretrotransposon event. Duplications have been associated with certaintypes of proliferative diseases. Duplications can be characterized usinggenomic microarrays or comparative genetic hybridization (CGH).

A genetic variation is sometimes an insertion. An insertion is sometimesthe addition of one or more nucleotide base pairs into a nucleic acidsequence. An insertion is sometimes a microinsertion. In someembodiments, an insertion comprises the addition of a segment of achromosome into a genome, chromosome, or segment thereof. In someembodiments, an insertion comprises the addition of an allele, a gene,an intron, an exon, any non-coding region, any coding region, segmentthereof or combination thereof into a genome or segment thereof. In someembodiments, an insertion comprises the addition (i.e., insertion) ofnucleic acid of unknown origin into a genome, chromosome, or segmentthereof. In some embodiments, an insertion comprises the addition (i.e.insertion) of a single base.

As used herein a “copy number variation” generally is a class or type ofgenetic variation or chromosomal aberration. A copy number variation canbe a deletion (e.g. micro-deletion), duplication (e.g., amicro-duplication) or insertion (e.g., a micro-insertion). Often, theprefix “micro” as used herein sometimes is a segment of nucleic acidless than 5 Mb in length. A copy number variation can include one ormore deletions (e.g. micro-deletion), duplications and/or insertions(e.g., a micro-duplication, micro-insertion) of a segment of achromosome. In some embodiments, a duplication comprises an insertion.In some embodiments, an insertion is a duplication. In some embodiments,an insertion is not a duplication. For example, often a duplication of asequence in a genomic section increases the counts for a genomic sectionin which the duplication is found. Often a duplication of a sequence ina genomic section increases the elevation. In some embodiments, aduplication present in genomic sections making up a first elevationincreases the elevation relative to a second elevation where aduplication is absent. In some embodiments, an insertion increases thecounts of a genomic section and a sequence representing the insertion ispresent (i.e., duplicated) at another location within the same genomicsection. In some embodiments, an insertion does not significantlyincrease the counts of a genomic section or elevation and the sequencethat is inserted is not a duplication of a sequence within the samegenomic section. In some embodiments, an insertion is not detected orrepresented as a duplication and a duplicate sequence representing theinsertion is not present in the same genomic section.

In some embodiments a copy number variation is a fetal copy numbervariation. Often, a fetal copy number variation is a copy numbervariation in the genome of a fetus. In some embodiments a copy numbervariation is a maternal copy number variation. In some embodiments, amaternal and/or fetal copy number variation is a copy number variationwithin the genome of a pregnant female (e.g., a female subject bearing afetus), a female subject that gave birth or a female capable of bearinga fetus. A copy number variation can be a heterozygous copy numbervariation where the variation (e.g., a duplication or deletion) ispresent on one allele of a genome. A copy number variation can be ahomozygous copy number variation where the variation is present on bothalleles of a genome. In some embodiments a copy number variation is aheterozygous or homozygous fetal copy number variation. In someembodiments a copy number variation is a heterozygous or homozygousmaternal and/or fetal copy number variation. A copy number variationsometimes is present in a maternal genome and a fetal genome, a maternalgenome and not a fetal genome, or a fetal genome and not a maternalgenome.

“Ploidy” refers to the number of chromosomes present in a fetus ormother. In some embodiments, “Ploidy” is the same as “chromosomeploidy”. In humans, for example, autosomal chromosomes are often presentin pairs. For example, in the absence of a genetic variation, mosthumans have two of each autosomal chromosome (e.g., chromosomes 1-22).The presence of the normal complement of 2 autosomal chromosomes in ahuman is often referred to as euploid. “Microploidy” is similar inmeaning to ploidy. “Microploidy” often refers to the ploidy of a segmentof a chromosome. The term “microploidy” sometimes refers to the presenceor absence of a copy number variation (e.g., a deletion, duplicationand/or an insertion) within a chromosome (e.g., a homozygous orheterozygous deletion, duplication, or insertion, the like or absencethereof). “Ploidy” and “microploidy” sometimes are determined afternormalization of counts of an elevation in a profile (e.g., afternormalizing counts of an elevation to an NRV of 1). Thus, an elevationrepresenting an autosomal chromosome pair (e.g., a euploid) is oftennormalized to an NRV of 1 and is referred to as a ploidy of 1.Similarly, an elevation within a segment of a chromosome representingthe absence of a duplication, deletion or insertion is often normalizedto an NRV of 1 and is referred to as a microploidy of 1. Ploidy andmicroploidy are often bin-specific (e.g., genomic section specific) andsample-specific. Ploidy is often defined as integral multiples of ½,with the values of 1, ½, 0, 3/2, and 2 representing euploidy (e.g., 2chromosomes), 1 chromosome present (e.g., a chromosome deletion), nochromosome present, 3 chromosomes (e.g., a trisomy) and 4 chromosomes,respectively. Likewise, microploidy is often defined as integralmultiples of ½, with the values of 1, ½, 0, 3/2, and 2 representingeuploidy (e.g., no copy number variation), a heterozygous deletion,homozygous deletion, heterozygous duplication and homozygousduplication, respectively.

In some embodiments, the microploidy of a fetus matches the microploidyof the mother of the fetus (i.e., the pregnant female subject). In someembodiments, the microploidy of a fetus matches the microploidy of themother of the fetus and both the mother and fetus carry the sameheterozygous copy number variation, homozygous copy number variation orboth are euploid. In some embodiments, the microploidy of a fetus isdifferent than the microploidy of the mother of the fetus. For example,sometimes the microploidy of a fetus is heterozygous for a copy numbervariation, the mother is homozygous for a copy number variation and themicroploidy of the fetus does not match (e.g., does not equal) themicroploidy of the mother for the specified copy number variation.

A microploidy is often associated with an expected elevation. Forexample, sometimes an elevation (e.g., an elevation in a profile,sometimes an elevation that includes substantially no copy numbervariation) is normalized to an NRV of 1 and the microploidy of ahomozygous duplication is 2, a heterozygous duplication is 1.5, aheterozygous deletion is 0.5 and a homozygous deletion is zero.

A genetic variation for which the presence or absence is identified fora subject is associated with a medical condition in certain embodiments.Thus, technology described herein can be used to identify the presenceor absence of one or more genetic variations that are associated with amedical condition or medical state. Non-limiting examples of medicalconditions include those associated with intellectual disability (e.g.,Down Syndrome), aberrant cell-proliferation (e.g., cancer), presence ofa micro-organism nucleic acid (e.g., virus, bacterium, fungus, yeast),and preeclampsia.

Non-limiting examples of genetic variations, medical conditions andstates are described hereafter.

Fetal Gender

In some embodiments, the prediction of a fetal gender or gender relateddisorder (e.g., sex chromosome aneuploidy) can be determined by a methodor apparatus described herein. In some embodiments, a method in whichfetal gender is determined can also comprise determining fetal fractionand/or presence or absence of a fetal genetic variation (e.g., fetalchromosome aneuploidy). Determining presence or absence of a fetalgenetic variation can be performed in a suitable manner, non-limitingexamples of which include karyotype analysis, amniocentesis, circulatingcell-free nucleic acid analysis, cell-free fetal DNA analysis,nucleotide sequence analysis, sequence read quantification, targetedapproaches, amplification-based approaches, mass spectrometry-basedapproaches, differential methylation-based approaches, differentialdigestion-based approaches, polymorphism-based approaches,hybridization-based approaches (e.g., using probes), and the like.

Gender determination generally is based on a sex chromosome. In humans,there are two sex chromosomes, the X and Y chromosomes. The Y chromosomecontains a gene, SRY, which triggers embryonic development as a male.The Y chromosomes of humans and other mammals also contain other genesneeded for normal sperm production. Individuals with XX are female andXY are male and non-limiting variations, often referred to as sexchromosome aneuploidies, include XO, XYY, XXX and XXY. In someinstances, males have two X chromosomes and one Y chromosome (XXY;Klinefelter's Syndrome), or one X chromosome and two Y chromosomes (XYYsyndrome; Jacobs Syndrome), and some females have three X chromosomes(XXX; Triple X Syndrome) or a single X chromosome instead of two (XO;Turner Syndrome). In some instances, only a portion of cells in anindividual are affected by a sex chromosome aneuploidy which may bereferred to as a mosaicism (e.g., Turner mosaicism). Other cases includethose where SRY is damaged (leading to an XY female), or copied to the X(leading to an XX male).

In certain cases, it can be beneficial to determine the gender of afetus in utero. For example, a patient (e.g., pregnant female) with afamily history of one or more sex-linked disorders may wish to determinethe gender of the fetus she is carrying to help assess the risk of thefetus inheriting such a disorder. Sex-linked disorders include, withoutlimitation, X-linked and Y-linked disorders. X-linked disorders includeX-linked recessive and X-linked dominant disorders. Examples of X-linkedrecessive disorders include, without limitation, immune disorders (e.g.,chronic granulomatous disease (CYBB), Wiskott-Aldrich syndrome, X-linkedsevere combined immunodeficiency, X-linked agammaglobulinemia, hyper-IgMsyndrome type 1, IPEX, X-linked lymphoproliferative disease, Properdindeficiency), hematologic disorders (e.g., Hemophilia A, Hemophilia B,X-linked sideroblastic anemia), endocrine disorders (e.g., androgeninsensitivity syndrome/Kennedy disease, KAL1 Kallmann syndrome, X-linkedadrenal hypoplasia congenital), metabolic disorders (e.g., ornithinetranscarbamylase deficiency, oculocerebrorenal syndrome,adrenoleukodystrophy, glucose-6-phosphate dehydrogenase deficiency,pyruvate dehydrogenase deficiency, Danon disease/glycogen storagedisease Type IIb, Fabry's disease, Hunter syndrome, Lesch-Nyhansyndrome, Menkes disease/occipital horn syndrome), nervous systemdisorders (e.g., Coffin-Lowry syndrome, MASA syndrome, X-linked alphathalassemia mental retardation syndrome, Siderius X-linked mentalretardation syndrome, color blindness, ocular albinism, Norrie disease,choroideremia, Charcot-Marie-Tooth disease (CMTX2-3),Pelizaeus-Merzbacher disease, SMAX2), skin and related tissue disorders(e.g., dyskeratosis congenital, hypohidrotic ectodermal dysplasia (EDA),X-linked ichthyosis, X-linked endothelial corneal dystrophy),neuromuscular disorders (e.g., Becker's muscular dystrophy/Duchenne,centronuclear myopathy (MTM1), Conradi-Hünermann syndrome,Emery-Dreifuss muscular dystrophy 1), urologic disorders (e.g., Alportsyndrome, Dent's disease, X-linked nephrogenic diabetes insipidus),bone/tooth disorders (e.g., AMELX Amelogenesis imperfecta), and otherdisorders (e.g., Barth syndrome, McLeod syndrome, Smith-Fineman-Myerssyndrome, Simpson-Golabi-Behmel syndrome, Mohr-Tranebjærg syndrome,Nasodigitoacoustic syndrome). Examples of X-linked dominant disordersinclude, without limitation, X-linked hypophosphatemia, Focal dermalhypoplasia, Fragile X syndrome, Aicardi syndrome, Incontinentiapigmenti, Rett syndrome, CHILD syndrome, Lujan-Fryns syndrome, andOrofaciodigital syndrome 1. Examples of Y-linked disorders include,without limitation, male infertility, retinits pigmentosa, andazoospermia.

Chromosome Abnormalities

In some embodiments, the presence or absence of a fetal chromosomeabnormality can be determined by using a method or apparatus describedherein. Chromosome abnormalities include, without limitation, a gain orloss of an entire chromosome or a region of a chromosome comprising oneor more genes. Chromosome abnormalities include monosomies, trisomies,polysomies, loss of heterozygosity, deletions and/or duplications of oneor more nucleotide sequences (e.g., one or more genes), includingdeletions and duplications caused by unbalanced translocations. Theterms “aneuploidy” and “aneuploid” as used herein refer to an abnormalnumber of chromosomes in cells of an organism. As different organismshave widely varying chromosome complements, the term “aneuploidy” doesnot refer to a particular number of chromosomes, but rather to thesituation in which the chromosome content within a given cell or cellsof an organism is abnormal. In some embodiments, the term “aneuploidy”herein refers to an imbalance of genetic material caused by a loss orgain of a whole chromosome, or part of a chromosome. An “aneuploidy” canrefer to one or more deletions and/or insertions of a segment of achromosome.

The term “monosomy” as used herein refers to lack of one chromosome ofthe normal complement. Partial monosomy can occur in unbalancedtranslocations or deletions, in which only a segment of the chromosomeis present in a single copy. Monosomy of sex chromosomes (45, X) causesTurner syndrome, for example.

The term “disomy” refers to the presence of two copies of a chromosome.For organisms such as humans that have two copies of each chromosome(those that are diploid or “euploid”), disomy is the normal condition.For organisms that normally have three or more copies of each chromosome(those that are triploid or above), disomy is an aneuploid chromosomestate. In uniparental disomy, both copies of a chromosome come from thesame parent (with no contribution from the other parent).

The term “euploid”, in some embodiments, refers a normal complement ofchromosomes.

The term “trisomy” as used herein refers to the presence of threecopies, instead of two copies, of a particular chromosome. The presenceof an extra chromosome 21, which is found in human Down syndrome, isreferred to as “Trisomy 21.” Trisomy 18 and Trisomy 13 are two otherhuman autosomal trisomies. Trisomy of sex chromosomes can be seen infemales (e.g., 47, XXX in Triple X Syndrome) or males (e.g., 47, XXY inKlinefelter's Syndrome; or 47, XYY in Jacobs Syndrome).

The terms “tetrasomy” and “pentasomy” as used herein refer to thepresence of four or five copies of a chromosome, respectively. Althoughrarely seen with autosomes, sex chromosome tetrasomy and pentasomy havebeen reported in humans, including)(XXX, XXXY, XXYY, XYYY, XXXXX, XXXXY,XXXYY, XXYYY and XYYYY.

Chromosome abnormalities can be caused by a variety of mechanisms.Mechanisms include, but are not limited to (i) nondisjunction occurringas the result of a weakened mitotic checkpoint, (ii) inactive mitoticcheckpoints causing non-disjunction at multiple chromosomes, (iii)merotelic attachment occurring when one kinetochore is attached to bothmitotic spindle poles, (iv) a multipolar spindle forming when more thantwo spindle poles form, (v) a monopolar spindle forming when only asingle spindle pole forms, and (vi) a tetraploid intermediate occurringas an end result of the monopolar spindle mechanism.

The terms “partial monosomy” and “partial trisomy” as used herein referto an imbalance of genetic material caused by loss or gain of part of achromosome. A partial monosomy or partial trisomy can result from anunbalanced translocation, where an individual carries a derivativechromosome formed through the breakage and fusion of two differentchromosomes. In this situation, the individual would have three copiesof part of one chromosome (two normal copies and the segment that existson the derivative chromosome) and only one copy of part of the otherchromosome involved in the derivative chromosome.

The term “mosaicism” as used herein refers to aneuploidy in some cells,but not all cells, of an organism. Certain chromosome abnormalities canexist as mosaic and non-mosaic chromosome abnormalities. For example,certain trisomy 21 individuals have mosaic Down syndrome and some havenon-mosaic Down syndrome. Different mechanisms can lead to mosaicism.For example, (i) an initial zygote may have three 21st chromosomes,which normally would result in simple trisomy 21, but during the courseof cell division one or more cell lines lost one of the 21stchromosomes; and (ii) an initial zygote may have two 21st chromosomes,but during the course of cell division one of the 21st chromosomes wereduplicated. Somatic mosaicism likely occurs through mechanisms distinctfrom those typically associated with genetic syndromes involvingcomplete or mosaic aneuploidy. Somatic mosaicism has been identified incertain types of cancers and in neurons, for example. In certaininstances, trisomy 12 has been identified in chronic lymphocyticleukemia (CLL) and trisomy 8 has been identified in acute myeloidleukemia (AML). Also, genetic syndromes in which an individual ispredisposed to breakage of chromosomes (chromosome instabilitysyndromes) are frequently associated with increased risk for varioustypes of cancer, thus highlighting the role of somatic aneuploidy incarcinogenesis. Methods and protocols described herein can identifypresence or absence of non-mosaic and mosaic chromosome abnormalities.

Tables 1A and 1B present a non-limiting list of chromosome conditions,syndromes and/or abnormalities that can be potentially identified bymethods and apparatus described herein. Table 1B is from the DECIPHERdatabase as of Oct. 6, 2011 (e.g., version 5.1, based on positionsmapped to GRCh37; available at uniform resource locator (URL)dechipher.sanger.ac.uk).

TABLE 1A Chromosome Abnormality Disease Association X XO Turner'sSyndrome Y XXY Klinefelter syndrome Y XYY Double Y syndrome Y XXXTrisomy X syndrome Y XXXX Four X syndrome Y Xp21 deletionDuchenne's/Becker syndrome, congenital adrenal hypoplasia, chronicgranulomatus disease Y Xp22 deletion steroid sulfatase deficiency Y Xq26deletion X-linked lymphproliferative disease  1 1p (somatic)neuroblastoma monosomy trisomy  2 monosomy growth retardation,developmental and mental delay, trisomy 2q and minor physicalabnormalities  3 monosomy Non-Hodgkin's lymphoma trisomy (somatic)  4monosomy Acute non lymphocytic leukemia (ANLL) trisomy (somatic)  5 5pCri du chat; Lejeune syndrome  5 5q myelodysplastic syndrome (somatic)monosomy trisomy  6 monosomy clear-cell sarcoma trisomy (somatic)  77q11.23 deletion William's syndrome  7 monosomy monosomy 7 syndrome ofchildhood; somatic: renal trisomy cortical adenomas; myelodysplasticsyndrome  8 8q24.1 deletion Langer-Giedon syndrome  8 monosomymyelodysplastic syndrome; Warkany syndrome; trisomy somatic: chronicmyelogenous leukemia  9 monosomy 9p Alfi's syndrome  9 monosomy 9pRethore syndrome partial trisomy  9 trisomy complete trisomy 9 syndrome;mosaic trisomy 9 syndrome 10 Monosomy ALL or ANLL trisomy (somatic) 1111p- Aniridia; Wilms tumor 11 11q- Jacobson Syndrome 11 monosomy myeloidlineages affected (ANLL, MDS) (somatic) trisomy 12 monosomy CLL,Juvenile granulosa cell tumor (JGCT) trisomy (somatic) 13 13q-13q-syndrome; Orbeli syndrome 13 13q14 deletion retinoblastoma 13monosomy Patau's syndrome trisomy 14 monosomy myeloid disorders (MDS,ANLL, atypical CML) trisomy (somatic) 15 15q11-q13 Prader-Willi,Angelman's syndrome deletion monosomy 15 trisomy (somatic) myeloid andlymphoid lineages affected, e.g., MDS, ANLL, ALL, CLL) 16 16q13.3deletion Rubenstein-Taybi monosomy papillary renal cell carcinomas(malignant) trisomy (somatic) 17 17p-(somatic) 17p syndrome in myeloidmalignancies 17 17q11.2 deletion Smith-Magenis 17 17q13.3 Miller-Dieker17 monosomy renal cortical adenomas trisomy (somatic) 17 17p11.2-12Charcot-Marie Tooth Syndrome type 1; HNPP trisomy 18 18p- 18p partialmonosomy syndrome or Grouchy Lamy Thieffry syndrome 18 18q- Grouchy LamySalmon Landry Syndrome 18 monosomy Edwards Syndrome trisomy 19 monosomytrisomy 20 20p- trisomy 20p syndrome 20 20p11.2-12 Alagille deletion 2020q- somatic: MDS, ANLL, polycythemia vera, chronic neutrophilicleukemia 20 monosomy papillary renal cell carcinomas (malignant) trisomy(somatic) 21 monosomy Down's syndrome trisomy 22 22q11.2 deletionDiGeorge's syndrome, velocardiofacial syndrome, conotruncal anomaly facesyndrome, autosomal dominant Opitz G/BBB syndrome, Caylor cardiofacialsyndrome 22 monosomy complete trisomy 22 syndrome trisomy

TABLE 1B Syndrome Chromosome Start End Interval (Mb) Grade 12q14microdeletion 12 65,071,919 68,645,525 3.57 syndrome 15q13.3 1530,769,995 32,701,482 1.93 microdeletion syndrome 15q24 recurrent 1574,377,174 76,162,277 1.79 microdeletion syndrome 15q26 overgrowth 1599,357,970 102,521,392 3.16 syndrome 16p11.2 16 29,501,198 30,202,5720.70 microduplication syndrome 16p11.2-p12.2 16 21,613,956 29,042,1927.43 microdeletion syndrome 16p13.11 recurrent 16 15,504,454 16,284,2480.78 microdeletion (neurocognitive disorder susceptibility locus)16p13.11 recurrent 16 15,504,454 16,284,248 0.78 microduplication(neurocognitive disorder susceptibility locus) 17q21.3 recurrent 1743,632,466 44,210,205 0.58 1 microdeletion syndrome 1p36 microdeletion 110,001 5,408,761 5.40 1 syndrome 1q21.1 recurrent 1 146,512,930147,737,500 1.22 3 microdeletion (susceptibility locus forneurodevelopmental disorders) 1q21.1 recurrent 1 146,512,930 147,737,5001.22 3 microduplication (possible susceptibility locus forneurodevelopmental disorders) 1q21.1 susceptibility 1 145,401,253145,928,123 0.53 3 locus for Thrombocytopenia- Absent Radius (TAR)syndrome 22q11 deletion 22 18,546,349 22,336,469 3.79 1 syndrome(Velocardiofacial/ DiGeorge syndrome) 22q11 duplication 22 18,546,34922,336,469 3.79 3 syndrome 22q11.2 distal 22 22,115,848 23,696,229 1.58deletion syndrome 22q13 deletion 22 51,045,516 51,187,844 0.14 1syndrome (Phelan- Mcdermid syndrome) 2p15-16.1 2 57,741,796 61,738,3344.00 microdeletion syndrome 2q33.1 deletion 2 196,925,089 205,206,9408.28 1 syndrome 2q37 monosomy 2 239,954,693 243,102,476 3.15 1 3q29microdeletion 3 195,672,229 197,497,869 1.83 syndrome 3q29 3 195,672,229197,497,869 1.83 microduplication syndrome 7q11.23 duplication 772,332,743 74,616,901 2.28 syndrome 8p23.1 deletion 8 8,119,29511,765,719 3.65 syndrome 9q subtelomeric 9 140,403,363 141,153,431 0.751 deletion syndrome Adult-onset 5 126,063,045 126,204,952 0.14 autosomaldominant leukodystrophy (ADLD) Angelman 15 22,876,632 28,557,186 5.68 1syndrome (Type 1) Angelman 15 23,758,390 28,557,186 4.80 1 syndrome(Type 2) ATR-16 syndrome 16 60,001 834,372 0.77 1 AZFa Y 14,352,76115,154,862 0.80 AZFb Y 20,118,045 26,065,197 5.95 AZFb + AZFc Y19,964,826 27,793,830 7.83 AZFc Y 24,977,425 28,033,929 3.06 Cat-EyeSyndrome 22 1 16,971,860 16.97 (Type I) Charcot-Marie- 17 13,968,60715,434,038 1.47 1 Tooth syndrome type 1A (CMT1A) Cri du Chat 5 10,00111,723,854 11.71 1 Syndrome (5p deletion) Early-onset 21 27,037,95627,548,479 0.51 Alzheimer disease with cerebral amyloid angiopathyFamilial 5 112,101,596 112,221,377 0.12 Adenomatous Polyposis HereditaryLiability 17 13,968,607 15,434,038 1.47 1 to Pressure Palsies (HNPP)Leri-Weill X 751,878 867,875 0.12 dyschondrostosis (LWD)-SHOX deletionLeri-Weill X 460,558 753,877 0.29 dyschondrostosis (LWD)-SHOX deletionMiller-Dieker 17 1 2,545,429 2.55 1 syndrome (MDS) NF1-microdeletion 1729,162,822 30,218,667 1.06 1 syndrome Pelizaeus- X 102,642,051103,131,767 0.49 Merzbacher disease Potocki-Lupski 17 16,706,02120,482,061 3.78 syndrome (17p11.2 duplication syndrome) Potocki-Shaffer11 43,985,277 46,064,560 2.08 1 syndrome Prader-Willi 15 22,876,63228,557,186 5.68 1 syndrome (Type 1) Prader-Willi 15 23,758,39028,557,186 4.80 1 Syndrome (Type 2) RCAD (renal cysts 17 34,907,36636,076,803 1.17 and diabetes) Rubinstein-Taybi 16 3,781,464 3,861,2460.08 1 Syndrome Smith-Magenis 17 16,706,021 20,482,061 3.78 1 SyndromeSotos syndrome 5 175,130,402 177,456,545 2.33 1 Split hand/foot 795,533,860 96,779,486 1.25 malformation 1 (SHFM1) Steroid sulphatase X6,441,957 8,167,697 1.73 deficiency (STS) WAGR 11p13 11 31,803,50932,510,988 0.71 deletion syndrome Williams-Beuren 7 72,332,74374,616,901 2.28 1 Syndrome (WBS) Wolf-Hirschhorn 4 10,001 2,073,670 2.061 Syndrome Xq28 (MECP2) X 152,749,900 153,390,999 0.64 duplication

Grade 1 conditions often have one or more of the followingcharacteristics; pathogenic anomaly; strong agreement amongstgeneticists; highly penetrant; may still have variable phenotype butsome common features; all cases in the literature have a clinicalphenotype; no cases of healthy individuals with the anomaly; notreported on DVG databases or found in healthy population; functionaldata confirming single gene or multi-gene dosage effect; confirmed orstrong candidate genes; clinical management implications defined; knowncancer risk with implication for surveillance; multiple sources ofinformation (OMIM, GeneReviews, Orphanet, Unique, Wikipedia); and/oravailable for diagnostic use (reproductive counseling).

Grade 2 conditions often have one or more of the followingcharacteristics; likely pathogenic anomaly; highly penetrant; variablephenotype with no consistent features other than DD; small number ofcases/reports in the literature; all reported cases have a clinicalphenotype; no functional data or confirmed pathogenic genes; multiplesources of information (OMIM, Genereviews, Orphanet, Unique, Wikipedia);and/or may be used for diagnostic purposes and reproductive counseling.

Grade 3 conditions often have one or more of the followingcharacteristics; susceptibility locus; healthy individuals or unaffectedparents of a proband described; present in control populations; nonpenetrant; phenotype mild and not specific; features less consistent; nofunctional data or confirmed pathogenic genes; more limited sources ofdata; possibility of second diagnosis remains a possibility for casesdeviating from the majority or if novel clinical finding present; and/orcaution when using for diagnostic purposes and guarded advice forreproductive counseling.

Preeclampsia

In some embodiments, the presence or absence of preeclampsia isdetermined by using a method or apparatus described herein. Preeclampsiais a condition in which hypertension arises in pregnancy (i.e.pregnancy-induced hypertension) and is associated with significantamounts of protein in the urine. In some instances, preeclampsia also isassociated with elevated levels of extracellular nucleic acid and/oralterations in methylation patterns. For example, a positive correlationbetween extracellular fetal-derived hypermethylated RASSF1A levels andthe severity of pre-eclampsia has been observed. In certain examples,increased DNA methylation is observed for the H19 gene in preeclampticplacentas compared to normal controls.

Preeclampsia is one of the leading causes of maternal and fetal/neonatalmortality and morbidity worldwide. Circulating cell-free nucleic acidsin plasma and serum are novel biomarkers with promising clinicalapplications in different medical fields, including prenatal diagnosis.Quantitative changes of cell-free fetal (cff)DNA in maternal plasma asan indicator for impending preeclampsia have been reported in differentstudies, for example, using real-time quantitative PCR for themale-specific SRY or DYS 14 loci. In cases of early onset preeclampsia,elevated levels may be seen in the first trimester. The increased levelsof cffDNA before the onset of symptoms may be due tohypoxia/reoxygenation within the intervillous space leading to tissueoxidative stress and increased placental apoptosis and necrosis. Inaddition to the evidence for increased shedding of cffDNA into thematernal circulation, there is also evidence for reduced renal clearanceof cffDNA in preeclampsia. As the amount of fetal DNA is currentlydetermined by quantifying Y-chromosome specific sequences, alternativeapproaches such as measurement of total cell-free DNA or the use ofgender-independent fetal epigenetic markers, such as DNA methylation,offer an alternative. Cell-free RNA of placental origin is anotheralternative biomarker that may be used for screening and diagnosingpreeclampsia in clinical practice. Fetal RNA is associated withsubcellular placental particles that protect it from degradation. FetalRNA levels sometimes are ten-fold higher in pregnant females withpreeclampsia compared to controls, and therefore is an alternativebiomarker that may be used for screening and diagnosing preeclampsia inclinical practice.

Pathogens

In some embodiments, the presence or absence of a pathogenic conditionis determined by a method or apparatus described herein. A pathogeniccondition can be caused by infection of a host by a pathogen including,but not limited to, a bacterium, virus or fungus. Since pathogenstypically possess nucleic acid (e.g., genomic DNA, genomic RNA, mRNA)that can be distinguishable from host nucleic acid, methods andapparatus provided herein can be used to determine the presence orabsence of a pathogen. Often, pathogens possess nucleic acid withcharacteristics unique to a particular pathogen such as, for example,epigenetic state and/or one or more sequence variations, duplicationsand/or deletions. Thus, methods provided herein may be used to identifya particular pathogen or pathogen variant (e.g. strain).

Cancers

In some embodiments, the presence or absence of a cell proliferationdisorder (e.g., a cancer) is determined by using a method or apparatusdescribed herein. For example, levels of cell-free nucleic acid in serumcan be elevated in patients with various types of cancer compared withhealthy patients. Patients with metastatic diseases, for example, cansometimes have serum DNA levels approximately twice as high asnon-metastatic patients. Patients with metastatic diseases may also beidentified by cancer-specific markers and/or certain single nucleotidepolymorphisms or short tandem repeats, for example. Non-limitingexamples of cancer types that may be positively correlated with elevatedlevels of circulating DNA include breast cancer, colorectal cancer,gastrointestinal cancer, hepatocellular cancer, lung cancer, melanoma,non-Hodgkin lymphoma, leukemia, multiple myeloma, bladder cancer,hepatoma, cervical cancer, esophageal cancer, pancreatic cancer, andprostate cancer. Various cancers can possess, and can sometimes releaseinto the bloodstream, nucleic acids with characteristics that aredistinguishable from nucleic acids from non-cancerous healthy cells,such as, for example, epigenetic state and/or sequence variations,duplications and/or deletions. Such characteristics can, for example, bespecific to a particular type of cancer. Thus, it is furthercontemplated that a method provided herein can be used to identify aparticular type of cancer.

Examples

The examples set forth below illustrate certain embodiments and do notlimit the technology.

Example 1: Capture of Nucleosomes to Enhance Fetal Fraction

In this example, a process is described for enriching the amount offetal derived DNA relative to total derived (maternal+fetal) DNA, alsoexpressed as fetal fraction, in plasma samples. DNA prepared from plasmais often referred to as circulating cell-free DNA (ccf DNA), asdescribed herein. Circulating cell-free DNA can exist in multiple stateswithin whole blood. DNA can be naked, histone bound (i.e., nucleosomescontaining DNA and histones), or encapsulated in a lipid bilayer as amicroparticle (for example, in an apoptotic structure). Circulating cellfree fetal DNA can be associated with microparticles and nucleosomes(e.g., histone bound) that are derived from fetal tissue. Circulatingcell free maternal DNA can be associated with microparticles andnucleosomes (histone bound) that are derived from maternal tissue. Thus,utilization of fetal source-specific antibodies to target fetal-derivedmicroparticles and/or nucleosomes can enrich fetal DNA. This exampledescribes a process for specifically enriching for circulating cell freefetal DNA associated nucleosomes (histone bound).

Nucleosome DNA typically is associated with an octamer of eight corehistones: H2A (2), H2B (2), H3 (2), and H4 (2); and a linker histone H1.In maternal blood and cleared plasma, fetal ccf DNA may have a loweroccupancy of H1 (i.e., a smaller percentage of the nucleosome DNA offetal origin may have H1 bound, relative to the percentage of maternalccf DNA having H1 bound). Without being limited by theory, the typicalsize distribution of fetal ccf DNA versus maternal ccf DNA is inaccordance with this concept, since nucleosome DNA without H1 bound maybe more susceptible to endonuclease digestion, thus resulting in shorterfragments.

Use of an antibody to histone H1 (e.g., without particular specificityto H1 subtypes or sources) can serve as a suitable negative selectionapproach to enrich for fetal DNA. Treatment of plasma with such antibodyin an immunoprecipitation (e.g., Chromatin ImmunoPrecipitation (CHIP))protocol can deplete maternal ccf DNA from the sample, thus enhancingccf DNA fetal fraction in the residual sample.

Antibodies to fetal-specific histones (e.g., H1.1, H1.3, H1.5), canenrich fetal ccf DNA when used in positive selection approaches.Antibodies to maternal-specific histones (e.g., H1.0), can enrich fetalccf DNA when used in depletion-based entichment (i.e., negativeselection) approaches. These approaches can include, conventionalimmunoprecipitation and Chromatin ImmunoPrecipitation (CHIP) approaches.Antibodies to H1M histone (expressed in Xenopus embryos) and to H1FOO(which are expressed in oocytes) may offer some cross reactivity andselectivity to human fetal-derived chromatin DNA, and thus also may beused as a positive selection strategy.

There are approximately eleven H1 variants, some of which may bespecific (or show preferential binding) to fetal-derived ccf DNA.Additionally, various maternal versus fetal differences in H3 histonesubtype can be exploited to enrich for fetal fraction. For example,antibodies recognizing conformational exposure differences for histoneH3.1 (e.g., differences between fetal and maternal H3.1) can be used forfetal DNA enrichment from plasma treated with such antibodies. Forexample, sequence variance (e.g., extra 10 amino acids at the c-terminusof fetal H3.1), and particular methylation of H3.1 in fetal versusmaternal can be exploited for fetal DNA enrichment.

Methods for identifying certain antibodies (e.g., selective forfetal-derived nucleosomes versus maternal-derived nucleosomes) fromcommercial or elicited populations of antibodies, antibody fragments oraptamers are described below.

Materials and Methods

Clinical samples derived from blood collected in STRECK cell free DNAblood collection tubes (BCTs) and processed to plasma are used. Samplescollected from pregnant and non-pregnant females are collected underappropriate review board approval with patient consent, and are includedin the investigations. Paired collections in additional blood collectiontubes (ACD, Heparin, PPAK, Streck® Cell free DNA BCT (containing acrosslinking agent and an anticoagulant (EDTA)) and other bloodcollection tubes known in the art) are included in evaluations, toimpact biomarker integrity. Plasma samples (pregnant and non-pregnant)are prepared from blood collected as above, or similar blood collectiontubes containing an anticoagulant, by centrifugation to remove cells.Typical centrifugation conditions are: 800 g to 16,000 g for 5-30 min.In certain instances, centrifugation conditions are: 800 g to 2500 g forup to 30 min followed by 2500 g to 12,000 g for up to 30 min. Longercentrifugation speeds also may be used. Prepared plasma can be utilizeddirectly for screening or enrichment, or can be frozen at −80° C. priorto use. For post freeze-thaw samples, an additional centrifugation stepof 800 to 16,000 g for up to 30 min, or 800 g to 2500 g for up to 30 minis performed. In certain instances, subsequent centrifugation is notperformed on post freeze-thaw samples.

Plasma samples may be subsequently subjected to crosslinking with afixative such as formaldehyde or glutaraldehyde or another aldehyde orcommonly known protein-protein or protein-DNA cross linking agent (e.g.,N-hydrosuccinamide), or an agent which releases such a fixative, if notalready included in blood collection tubes. Such processing can affectcrosslinking to reinforce DNA-histone interaction prior to selectivebinding with targeted antibodies. Samples collected in a bloodcollection tube (BCT) containing a fixative such as formaldehyde orglutaraldehyde or another aldehyde or aldehyde releaser or other knownprotein-protein or protein-DNA cross linking agent, may not requireadditional fixation prior to binding with antibodies, however suchfixation may be used in certain instances. For example, samplescollected in Streck® Cell-free DNA BCT may not require additionalfixation prior to reaction with antibodies. If conditions close tophysiologic normal with respect to pH (e.g., pH 6 to pH 8) and ionicstrength normal are utilized for all processing steps, crosslinking maynot be necessary regardless of BCT (e.g., solutions containing 140 mMsodium ion, 100 mM chloride ion, 25 mM carbonate, or having an overallmolarity of 35 mM to 350 mM).

Antibodies to H1.1, H1.3, and/or H1.5 are investigated in positiveselection approaches for fetal derived ccf DNA. Antibodies to H1.0and/or H1 are targeted for depletion-based enrichment (negativeselection) approaches. Antibodies to H1M histone (expressed in Xenopusembryos) and to H1FOO (expressed in oocytes) may cross react with humansource material and thus offer selectivity to human fetal derivedchromatin DNA. Such antibodies may be useful for a fetal ccf DNApositive selection strategy. There are eleven H1 variants characterized,and some may be specific (or show preferential binding) to ccf DNA offetal source as outlined above. In addition, the use of an antibody toH1, without particular specificity may serve a suitable negativeselection approach. Treatment of cleared plasma with one or more suchantibodies in an immunoprecipitation protocol can effect significantdepletion of maternal ccf DNA from a sample, thus enhancing ccf DNAfetal fraction.

Additionally, various maternal versus fetal differences in H3 histonesubtype are exploited to enrich for fetal fraction. For example,antibodies recognizing one or more histone H3.1 conformational exposuredifferences in fetal versus maternal (e.g., sequence variance (e.g.,extra 10 amino acids at the c-terminus of fetal H3.1), and particularmethylation differences) are used for fetal DNA enrichment from plasmatreated with such antibodies.

Certain antibodies are identified via assays using plasma samplesprocessed as described above. ELISA, western blotting, Luminex or othersimilar approaches are used to rapidly test antibody selectivity. Insuch an assay system, selectivity for fetal or maternal specific ccf DNAinitially is assessed based on cross reactivity to plasma samplesderived from pregnant and non-pregnant women. Antibodies thatdemonstrate an ability to preferentially react with plasma derived frompregnant rather non-pregnant samples offer a degree of selectivity forfetal nucleosomes and thus are useful for positive selection approaches.Such antibodies are prioritized for preparative methods (e.g.,immunoprecipitation) to enrich for fetal fraction. Antibodies that reactacross both sample types may be maternal specific and may bind onlymaternal ccf DNA (nucleosome bound), and thus are suitable to negativeselection approaches (i.e., enrichment of fetal ccf DNA by depletion ofmaternal ccf DNA). Antibodies that react across both pregnant andnon-pregnant samples, in certain instances, are further characterizedand distinguished with respect to specificity (fetal versus maternal) bytesting with DNA samples derived from peripheral blood mononuclear cells(PBMC) isolated from “buffy coat”. Further validation of antibodyhistone selectivity is performed, in certain instances, usingimmunoprecipitation approaches and analysis of DNA fragments resultingfrom enrichment approaches. Sequencing and/or fetal specific assays suchas FQA (fetal quantifier assay, for both male or/female fetuses) and/orqPCR assay (applicable to male fetuses) are further be used to validatespecificity of antibodies, in certain instances.

Several ELISA assay formats are used for screening. Typical assayprocedures are outlined here. After initial washes, a micro titer plateor other surface is first coated with a DNA binding protein or a histonebinding antibody. The primary histone antibody should bind to any one ofthe 4 primary core histone types: H2A, H2B, H3, H4, to afford capture ofall nucleosome DNA. This antibody should not be selective to specifichistone subtypes or posttranslational modifications thereof to avoidtissue or cell cycle specificity. Similarly, the DNA binding proteinshould be non-specific to afford capture of all nucleosome DNA.Following several washes with buffer at neutral (or near neutral) pH andwith similar physical isotonic strength, blocking with an agent such ascasein or a bovine serum albumin containing agent is performed.Following several washes with buffer at neutral (or near neutral) pH andwith similar physical isotonic strength, a portion of analyte plasma(either maternal pregnant (positive control) or non-pregnant (negativecontrol)) is applied to each well. Capture of nucleosome DNA is achievedby incubation for at least 2 min at ambient temperature or afterincubation at temperatures as high as 42° C. Following several washeswith buffer at neutral (or near neutral) pH and with similar physiologicionic strength, each of the antibodies tested for fetal histone orhistone specific primary binding is applied to each well. This mixtureis subjected to incubation typically for at least 2 min at ambienttemperature or after incubation at temperatures as high as 42° C. Suchprimary antibody is typically labeled with biotin or another agent. Suchprimary antibody is unlabeled, in certain instances, in which case anisotype (species) specific antibody of different isotype (species) isused as the secondary antibody. In this step, only samples andantibodies with matched specificity will react with the primaryantibody. Following several washes with buffer at neutral (or nearneutral) pH and with similar physiological ionic strength, excessprimary antibody is removed for each well. The secondary antibody,specific to either the label (e.g. streptavidin to biotin) to theisotype (species) of the primary antibody is then applied. The secondaryantibody is directly labeled with a colorimetric or fluorescentlylabeled dye, in certain instances, or more typically is labeled with anenzyme which can convert a non-colorimetric or non-fluorescent agent toone that is visualized via colorimetric or fluorescent means. Thesecondary antibody is subjected to incubation typically for at least 2min at ambient temperature or after incubation at temperatures as highas 42° C. Following several washes with buffer at neutral (or nearneutral) pH and with similar physical ionic strength, excess secondaryantibody is removed for each well. Following this step, a reportingagent is added. For example, an ABTS reagent mixture is added to aperoxidase labeled secondary antibody system. The color is allowed todevelop and subsequently measured spectrophotometrically.

Rather than using a solid support for capture of the nucleosomes, a beador microparticle (e.g., magnetic or non-magnetic) is used in certaininstances. Rather than using a soluble antibody, an antibody conjugatedto or adsorbed onto a bead or microparticle is substituted to affordcapture, in certain instances. Either a primary or secondary antibodycan be conjugated or otherwise associated with the bead. For bead basedsolid support systems, analysis is conducted using a flow cytometer, incertain instances.

For methods where secondary colorimetric or fluorescent analysis is notrequired, one antibody specific to the captured material (e.g.,nucleosomal DNA) is used, in certain instances. The antibody is labeledwith streptavidin and captured with biotin labeled beads, in certaininstances. Such a system allows preparative isolation of targetednucleosome DNA.

In certain instances, a bead or microparticle is used to facilitateisolation of material with DNA having an enriched fetal fraction ofnucleosomes (histone bound DNA), either via sedimentation (e.g., gravitysedimentation or centrifugation) or via separation with a magnet tocollect magnetic beads. In certain instances, nucleosome ccf DNA isselected via positive selection with an antibody targeted to one or morefetal specific histones (as described above) and is separated from thebulk solution and washed of impurities with several washes with bufferat neutral (or near neutral) pH and with similar physical ionicstrength. Nucleosome ccf DNA enriched with respect to fetal fraction isthen eluted from the bead by adding an excess of competitor affinity tagto the system (e.g. in the case of biotin/streptavidin based binding,adding an excess of biotin labeled beads to an antibody conjugated tostreptavidin (or visa versa)). Release is achieved with excess biotin orexcess streptavidin, in certain instances. DNA is taken directly using aDNA extraction protocol (e.g., Qiagen circulating nucleic acid kit), incertain instances.

In certain instances, nucleosome ccf DNA is selected via negativeselection with an antibody targeted to one or more maternal specifichistones (as described above). In such instances, the maternalnucleosome DNA is separated from the bulk plasma, which contains ccf DNAdepleted of maternal nucleosome bound DNA and the residual bulk plasmais enriched with respect to fetal DNA. The plasma sample is thenprocessed via DNA extraction or direct analysis in amplification based(PCR) or sequencing approaches, in certain instances. DNA extraction isachieved using an extraction system such as the Qiagen circulatingnucleic acid kit, in certain instances.

Several ELISA based assays for nucleosome detection are commerciallyavailable. These include, for example, Cell Death Detection ELISA-PLUSsystem (Roche) and QIA25 nucleosome ELISA kit (EMD Millipore,Calbiochem). Such assays can be modified to include specificanti-histone antibodies (fetal-specific or maternal-specific asdescribed herein) to identify and validate fetal versus maternalspecificity.

Antibodies useful for maternal nucleosome DNA depletion (negativeselection) include but are not limited to: Abcam Anti-Histone H1antibody [1415-1]-Carboxyterminal end (ab62884), Abcam anti-histone H1.0antibody (EPR6536) (ab134914), Abcam anti-histone H1 antibody (EPR6537)(ab125027), uniProt Antibody P10412, Histone H1.4 aka H1b, H1s4.

Antibodies useful for fetal nucleosome DNA enrichment (positiveselection) include: Abcam Ltd. (Cambridge, UK): Anti-Histone H1.3antibody H1.3 (ab24174), Anti-Histone H1.1 antibody H1.1 (ab17584), andAnti-Histone H1.5 antibodies H1.5 (ab24175), H1.5 (ab18208), NovusBiologics, Histone H1.3 Antibody (NBP1-41140), Abcam Ltd. (Cambridge,UK): H1.3 (ab24174) Fitzgerald, Histone H3.1 antibody (Phospho-Thr3)(70R-11156), Histone H3.1 antibody (70R-11159).

In some instances, placental villi tissue is isolated, and nuclei andcontained chromatin and nucleosomes are prepared. This material issubsequently conjugated or combined with an adjuvant such as KLH toimmunize rodents and illicit an immune response and thus generateantibodies. Monocolonal antibodies are isolated through methods that arewell described in the literature. Such monoclonal antibodies arescreened in ELISA as described above, with pregnant and nonpregnantplasma samples or via phage display.

Example 2: Fetal DNA Enrichment by Ultracentrifugation

In this example, the amount of fetal DNA and maternal DNA in circulatingmicroparticles and in the “soluble” phase (i.e. not in microparticles)was estimated in pooled plasma samples from pregnant females. Plasmafrom pregnant subjects typically contains “free” DNA, nucleosomal DNAand DNA enclosed in circulating microparticles (e.g., apoptotic bodies)and collectively is termed ccfDNA. Ultracentrifugation can enrichcirculating microparticles (cMPs) of different size (e.g., exosomes(about 70-120 nm diameter; carrying mainly RNA) from apoptotic bodies(about 300 nm to greater than about 1000 nm). About 90% of circulatingapoptotic bodies contain DNA and about 10% contain RNA, typically withno mixed nucleic acid-containing particles. If the majority of apoptoticbodies at 10 to 12 weeks of pregnancy are of fetal origin, then thepurification of apoptotic bodies is a means for enriching fetal DNA.Fractionation of subcellular structures by centrifugation at selectedg-forces and sucrose (or PERCOLL) density centrifugation are used, incertain instances. Explanations for certain abbreviations and specialistterms used in this example are presented in Table 2 below.

TABLE 2 Abbreviations and specialist terms Abbreviation or specialistterm Explanation ACD-A Tubes Acid citrate dextrose (type A) bloodcollection tubes BCT Blood Collection Tube ccf DNA Circulating cell-freeDNA ccff DNA Circulating cell-free fetal DNA EDTAEthylenediaminetetraacetic acid, anti-coagulant commonly used in bloodcollection tubes rxn Reaction SCAT PPACK BCT SampleCollection/Anticoagulant Tubes (A.K.A. SCAT-875B BCT) with 75 μM PPACKprotease inhibitor Streck Tubes Streck Cell-Free DNA Blood CollectionTubes

Fetal DNA Enrichment by Ultracentrifugation (N=2)

In certain instances, the amount of fetal DNA and maternal DNA incirculating microparticles and in the “soluble” phase (i.e. not inmicroparticles) was estimated in pooled plasma samples from pregnantfemales using a small collection of samples (sometimes referred to asthe “pre-test”). To show that fetal DNA is enriched in apoptotic bodies,cMPs in pooled plasma samples (N=2) were separated byultracentrifugation. DNA was extracted from resulting supernatants andpellets, and quantified by qPCR assays (e.g., for β-globin and DYS1).Fetal fraction of supernatants and pellets were calculated so that fetalDNA enrichment, if present, was recorded. The majority of fetal DNA(74%) and total DNA (70%) of the original plasma (noultracentrifugation) was in the “soluble” state, and not in the pellet,i.e. in cMPs. The distribution of total DNA and fetal DNA in the 25K×gpellet was 62% to 38%. Smaller exosomes typically do not harbor DNA butrather RNA. After centrifugation of the 25K supernatant at 100K×g theresults showed a distribution of 82% of total DNA in the supernatant and18% in the pellet, supporting the notion that particles (chieflyexosomes) in the 100K pellet may not contain large amounts of theavailable circulating DNA. The fetal fraction for the no-spin controlwas 0.06, for the 25K×g supernatant was 0.07 and for the 100K×gsupernatant was 0.06. The fetal copy numbers in the pellets were too lowto allow for sensible fetal fraction calculations.

Fetal DNA Enrichment by Ultracentrifugation

In certain instances, the amount of fetal DNA and maternal DNA incirculating microparticles and in the “soluble” phase (i.e. not inmicroparticles) was estimated in pooled plasma samples from pregnantfemales using a larger collection of samples. To show that fetal DNA isenriched in apoptotic bodies, the fetal fraction of appropriateultracentrifugation supernatants and pellets was calculated.

Materials and Methods

Certain observations, predictions and/or conclusions were made whendesigning the assay below. For example, certain centrifugationconditions (e.g., 25,000×g for 1 hour) can sediment apoptotic bodies andlarger, subcellular structures that do not get removed by priorcentrifugations (e.g., 1600×g for 15 minutes and 2500×g for 10 minutes),in certain instances. The majority of enclosed fetal DNA resides inapoptotic bodies and not in other subcellular structures, in certaininstances. The pre-test described above with 2×4 mL samples in replicate(16 mL total) was limited by a low sample number. For fetal DNAquantification the qPCR assay used was limited to the presence ofY-chromosomes (male fetus). Fetal DNA assayed by qPCR was corrected by afactor of 2 to reflect an estimated 50% male contribution in Super Pool12.

Maternal peripheral blood was collected into three types of bloodcollection tubes (BCTs): SCAT PPACK BCT (1×), STRECK Cell-Free DNA BCT(2× STRECK Tubes) and ACD-A Tubes (2×). Within 6 hours plasma wasproduced using the standard STRECK Tube protocol: 1600×g for 15 minutes,removal of plasma, followed by 2500×g for 10 minutes, followed by frozenstorage of the plasma samples. In some instances, plasma from STRECKSuper Pool 12 (pregnant subjects, mainly at 10 to 12 weeks of gestation)was used immediately after the pool was created (24 mL), i.e., theplasma samples did not experience the standard freezing step.

To maintain the same experimental conditions, the “fresh” (frozen onlyonce) plasma samples were centrifuged at 1600×g for 10 minutes at 4° C.to remove potential debris. The cleared plasma was used forultracentrifugation studies.

The qPCR assays for total DNA and fetal DNA in supernatants and pellets(input: 5 μL each) were run in quadruplicate reactions in separatewells. Supernatant qPCR results were expressed in copies/reaction (5 μLout of (53/4) μL, representing 37.6% of 1 mL plasma or 9.4% of 4 mLplasma). Conversion of copies/rxn to copies/mL was done by multiplyingby 2.66. Pellet qPCR results were expressed in copies/rxn (5 μL out of40 μL). In this instance, conversion of pellet copies/rxn to pelletcopies/mL of plasma was done by multiplying by 2. FQA4b data for SuperPool 12 samples were expressed in copies/mL of plasma. A summary ofassay reagents, instrumentation and software used in this example isprovided in Table 4 below.

TABLE 4 Assay reagents, instrumentation, and software used Item VendorCatalog # Reagents Express qPCR Master Mix Life Technology TaqMan HumanMale Genomic Control Life Technology 4312660 DNA 50bp DNA Ladder (50 μg,1 μg/μL)) Life Tech/Invitrogen 10416-014 DNase I VWR PI90083 QIAamp DSPCirculating NA Kit QIAGEN 61504 Labware Streck Cell-Free DNA BCT Streck218962 SCAT PPACK BCT 10 mL Haematologic SCAT-875B Technologies ACD-ATubes 8.5 mL VWR VT4606 Instrumentation Centrifuge for 96-well platesBeckman n/a Microcentrifuge for 1.5 mL and 2 mL VWR n/a tubes Vortex VWRn/a ViiA 7 Real-Time PCR System with Life Technology 4453536 384-WellBlock Software MassARRAY ™ Nanodispenser, version Sequenom Version 1.2.11.2.1 (RS1000) (RS1000) MassARRAY ™ Analyzer Workstation, Sequenomincludes: ChipLinker Sequenom Version 20.0.1 AnalyzerControl SequenomVersion 2.3.45 SpectroCALLER Sequenom Version 3.4.1.42R SpectroACQUIRE,version 4.0.2.52 Sequenom Version 4.0.2.52 TypePLEX ™ MassARRAY ™ TyperSequenom n/a 4.0 Software ViiA 7 Life Technology Version 1.2 PCR PrimerOligos IDT Lot# 5510202

Results

DNA from Super Pool 12 plasma samples (frozen only once) was extractedusing the standard QIAGEN CNA procedure and served as the reference forultracentrifugation conditions. As determined by qPCR, the originalplasma average was 42 fetal copies/rxn. In comparison, the 25Ksupernatant had 34 copies/rxn and the 25K pellets had 3 copies/rxn for atotal of 37 fetal copies/rxn, compared to the original 42 fetal copies.The 100K supernatant had 31 copies/rxn and the 100K pellet had 1copy/rxn for a total of 32 copies/rxn, again compared to the original 42fetal copies. In contrast, for FQA4b the fetal copy number was 334copies/mL in the pre-freeze sample (FIG. 2).

For assessment of total copies, the original plasma average was 698total DNA copies/rxn. In comparison, the 25K supernatant had 522 totalDNA copies/rxn and the 25K pellets had 322 copies/rxn for a total of 844fetal copies/rxn, compared to the original 522 fetal copies. The 100Ksupernatant had 489 total DNA copies/rxn and the 100K pellet had 107total DNA copies/rxn for a total of 596 total DNA copies/rxn, comparedto the original 698 total DNA copies. In contrast, for FQA4b the totalDNA copy number was 5376 copies/mL in the pre-freeze sample (FIG. 3).

Fetal Fraction in the original plasma was an average 0.06. In the 25KSupernatant the Fetal Fraction was 0.07 and in the corresponding Pelletit was 0.01 (Note: Only 3 fetal copies were detected and used in thecalculation for Fetal Fraction in the pellet). The Fetal Fraction in the100K Supernatant was 0.06 and 0.01 (Note: Only 1 fetal copy was detectedand used in the calculation for Fetal Fraction in the pellet) in the100K Pellet. In contrast, for FQA4b the Fetal Fraction using FQA4b was0.07 (FIG. 4).

Mean total copies or mean fetal copies from supernatants (S) and pellets(P) were calculated for each condition. For the no-treatment control(Super Pool 12) only the supernatant was used (FIG. 5, columns 2 and 3of the table). The grand total for each condition was calculated (FIG.5, column 4 of the table). If there were no losses and the assays hadhigh accuracy, these three numbers should not be different. Thedistribution of total and fetal DNA in supernatant and pellet for thetwo centrifugation conditions also was calculated (FIG. 5, columns 5 and6 of the table). After the 25K×g centrifugation, 62% of total DNA wasfound in the supernatant and 38% in the pellet; the distribution changedafter the 100K×g centrifugation to 82% and 18%, respectively.

The recovery of “soluble” total and fetal DNA was estimated by comparingthe copy numbers per reaction for the no-spin, 25K and 100Kcentrifugation conditions. After the 25K×g centrifugation, 75% of totaland 83% of fetal DNA were recovered in the supernatant (FIG. 6). A 6%loss of total DNA and a 10% loss of fetal DNA in the supernatant wereobserved after the 100K×g centrifugation step.

Overall, 70% of total DNA and 74% of fetal DNA were recovered fromsupernatants.

Additionally, when comparing total and fetal copy number quantificationby the two assays, qPCR assay and FQA4b, 27% of total DNA and 14% offetal DNA in the plasma were recovered. Post-freeze values for FQA4bwere used here, because of the additional 1600×g spin in both protocols(FIG. 6; SP 12=Super Pool 12).

Example 3: Examples of Embodiments

A1. A method for enriching fetal nucleic acid in sample nucleic acidthat includes fetal nucleic acid and maternal nucleic acid, comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample from a pregnant female, which sample nucleic        acid comprises vesicle-free nucleic acid and vesicular nucleic        acid; and    -   (b) separating some or substantially all of the vesicular        nucleic acid from the sample nucleic acid, thereby generating a        separation product enriched for the vesicle-free nucleic acid,        wherein fetal nucleic acid in the separation product is enriched        relative to fetal nucleic acid in the sample nucleic acid.

A2. The method of embodiment A1, comprising (c) analyzing nucleic acidin the separation product.

B1. A method which comprises analyzing nucleic acid in a separationproduct prepared by a process comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample from a pregnant female, which sample nucleic        acid comprises vesicle-free nucleic acid, vesicular nucleic        acid, maternal nucleic acid and fetal nucleic acid; and    -   (b) separating some or substantially all of the vesicular        nucleic acid from the sample nucleic acid, thereby generating a        separation product enriched for the vesicle-free nucleic acid,        wherein the fetal nucleic acid in the separation product is        enriched relative to the fetal nucleic acid in the sample        nucleic acid.

C1. A method for enriching vesicle-free nucleic acid in sample nucleicacid, comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample, which sample nucleic acid comprises        vesicle-free nucleic acid and vesicular nucleic acid; and    -   (b) separating some or substantially all of the vesicular        nucleic acid from the sample nucleic acid, thereby generating a        separation product, wherein vesicle-free nucleic acid in the        separation product is enriched relative to vesicle-free nucleic        acid in the sample nucleic acid.

C2. The method of embodiment C1, comprising (c) analyzing nucleic acidin the separation product.

D1. A method which comprises analyzing nucleic acid in a separationproduct prepared by a process comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample, which sample nucleic acid comprises        vesicle-free nucleic acid and vesicular nucleic acid; and    -   (b) separating some or substantially all of the vesicular        nucleic acid from the sample nucleic acid, thereby generating a        separation product, wherein vesicle-free nucleic acid in the        separation product is enriched relative to vesicle-free nucleic        acid in the sample nucleic acid.

D2. A method for enriching fetal nucleic acid in sample nucleic acidthat includes fetal nucleic acid and maternal nucleic acid, comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample from a pregnant female, which sample nucleic        acid comprises maternal-derived vesicular nucleic acid and        fetal-derived vesicular nucleic acid; and    -   (b) separating some or substantially all of the maternal-derived        vesicular nucleic acid from the fetal-derived vesicular nucleic        acid, thereby generating a separation product enriched for the        fetal-derived vesicular nucleic acid, wherein fetal nucleic acid        in the separation product is enriched relative to fetal nucleic        acid in the sample nucleic acid.

D3. A method for enriching fetal nucleic acid in sample nucleic acidthat includes fetal nucleic acid and maternal nucleic acid, comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample from a pregnant female, which sample nucleic        acid comprises vesicle-free nucleic acid and vesicular nucleic        acid; and    -   (b) separating some or substantially all of the vesicular        nucleic acid from the sample nucleic acid, thereby generating a        separation product enriched for the vesicular nucleic acid,        wherein fetal nucleic acid in the separation product is enriched        relative to fetal nucleic acid in the sample nucleic acid.

D4. The method of embodiment D2 or D3, comprising (c) analyzing nucleicacid in the separation product.

E1. The method of any one of embodiments A1 to D4, wherein separatingsome or substantially all of the vesicular nucleic acid from the samplenucleic acid comprises filtering the sample nucleic acid.

E2. The method of any one of embodiments A1 to D4, wherein separatingsome or substantially all of the vesicular nucleic acid from the samplenucleic acid comprises centrifuging the sample nucleic acid.

E2.1 The method of embodiment E2, wherein centrifuging the samplenucleic acid comprises use of ultracentrifugation.

E3. The method of any one of embodiments A1 to D4, wherein separatingsome or substantially all of the vesicular nucleic acid from the samplenucleic acid comprises contacting the sample nucleic acid with an agentthat specifically binds to vesicles comprising the vesicular nucleicacid.

E3.1 The method of embodiment D2, wherein separating some orsubstantially all of the maternal-derived vesicular nucleic acid fromthe fetal-derived vesicular nucleic acid comprises contacting the samplenucleic acid with an agent that specifically binds to maternal-derivedvesicular nucleic acid.

E3.2 The method of embodiment D2, wherein separating some orsubstantially all of the maternal-derived vesicular nucleic acid fromthe fetal-derived vesicular nucleic acid comprises contacting the samplenucleic acid with an agent that specifically binds to fetal-derivedvesicular nucleic acid.

E4. The method of embodiment E3 or E3.1, wherein the agent specificallybinds to vesicles from hemopoietic tissue.

E5. The method of embodiment E4, wherein the agent specifically binds tovesicles from red blood cells.

E6. The method of embodiment E5, wherein the agent specifically binds toCD235a.

E7. The method of embodiment E4, wherein the agent specifically binds tovesicles from leukocytes.

E8. The method of embodiment E7, wherein the agent specifically binds toCD45.

E9. The method of embodiment E4, wherein the agent specifically binds tovesicles from lymphocytes.

E10. The method of embodiment E9, wherein the agent specifically bindsto a vesicular component chosen from CD4, CD8 and CD20.

E11. The method of embodiment E4, wherein the agent specifically bindsto vesicles from granulocytes.

E12. The method of embodiment E11, wherein the agent specifically bindsto CD66b.

E13. The method of embodiment E4, wherein the agent specifically bindsto vesicles from monocytes.

E14. The method of embodiment E13, wherein the agent specifically bindsto CD14.

E15. The method of embodiment E4, wherein the agent specifically bindsto vesicles from platelets.

E16. The method of embodiment E15, wherein the agent specifically bindsto a vesicular component chosen from CD31, CD41, CD41a, CD42a, CD42b,CD61 and CD62P.

E17. The method of embodiment E3 or E3.1, wherein the agent specificallybinds to vesicles from endothelial cells.

E18. The method of embodiment E17, wherein the agent specifically bindsto a vesicular component chosen from CD31, CD34, CD54, CD62E, CD51,CD105, CD106, CD144 and CD146.

E18.1. The method of any one of embodiment E3 to E18, wherein generatingthe separation product comprises separating components bound by theagent away from the sample nucleic acid.

E19. The method of any one of embodiments A1 to E18.1, whereinseparating some or substantially all of the vesicular nucleic acid fromthe sample nucleic acid further comprises contacting the sample nucleicacid with an agent that specifically binds to a histone associated withvesicle-free nucleic acid.

E19.1 The method of embodiment E19, wherein the agent specifically bindsto histone H3.3.

E20. The method of embodiment E19, wherein the agent specifically bindsto histone H1.

E20.1 The method of embodiment E20, wherein the histone H1 isunmethylated.

E20.2. The method of embodiment E19 or E20.1, wherein generating theseparation product comprises separating components bound by the agentaway from the sample nucleic acid.

E20.3. The method of any one of embodiments E3 to E20.2, wherein theagent is an antibody.

E21. The method of any one of embodiments A1 to E20.3, wherein thevesicular nucleic acid is within a vesicle having a diameter of lessthan about 1 micrometer.

E22. The method of embodiment E21, wherein the diameter is about 10nanometers to about 600 nanometers.

E23. The method of embodiment E22, wherein the diameter is about 40nanometers to about 100 nanometers.

E24. The method of any one of embodiments A1 to E23, wherein the samplenucleic acid is from blood plasma.

E25. The method of any one of embodiments A1 to E23, wherein the samplenucleic acid is from blood serum.

E26. The method of any one of embodiments A1 to E25, wherein obtainingthe sample nucleic acid comprises subjecting the biological sample to anin vitro process that isolates the sample nucleic acid from other samplecomponents.

E27. The method of any one of embodiments A1 to E25, wherein theseparation product comprises about 50% or greater vesicle-free nucleicacid.

E28. The method of any one of embodiments A2, B1, C2, D1, D4 and E1 toE27, wherein analyzing the nucleic acid in the separation productcomprises subjecting the nucleic acid to an in vitro sequencing process.

E29. The method of embodiment E28, wherein the sequencing processprovides sequence reads.

E30. The method of embodiment E29, comprising mapping the sequence readsto a reference sequence.

E31. The method of embodiment E30, comprising counting the sequencereads mapped to the reference sequence.

E32. The method of embodiment E31, comprising utilizing the countedsequence reads to generate an outcome determinative of the presence orabsence of a genetic variation.

E33. The method of embodiment E32, wherein the genetic variation is acopy number variation.

E34. The method of embodiment E32 or E33, wherein the genetic variationis a chromosome aneuploidy.

E35. The method of embodiment E34, wherein the chromosome aneuploidy isa chromosome 21 aneuploidy.

F1. A method for enriching fetal nucleic acid in sample nucleic acidthat includes fetal nucleic acid and maternal nucleic acid, comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample from a pregnant female, which sample nucleic        acid comprises a first histone-associated nucleic acid species        and a second histone-associated nucleic acid species; and    -   (b) separating some or substantially all of the first        histone-associated nucleic acid species from the sample nucleic        acid, thereby generating a separation product enriched for the        second histone-associated nucleic acid species, wherein fetal        nucleic acid in the separation product is enriched relative to        fetal nucleic acid in the sample nucleic acid.

F2. The method of embodiment F1, comprising (c) analyzing nucleic acidin the separation product.

G1. A method which comprises analyzing nucleic acid in a separationproduct prepared by a process comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample from a pregnant female, which sample nucleic        acid comprises a first histone-associated nucleic acid species,        a second histone-associated nucleic acid species, maternal        nucleic acid and fetal nucleic acid; and    -   (b) separating some or substantially all of the first        histone-associated nucleic acid species from the sample nucleic        acid, thereby generating a separation product enriched for the        second histone-associated nucleic acid species, wherein the        fetal nucleic acid in the separation product is enriched        relative to the fetal nucleic acid in the sample nucleic acid.

G2. The method of any one of embodiments F1 to G1, comprising lysingvesicles present in the sample nucleic acid.

H1. A method for enriching a histone-associated nucleic acid species insample nucleic acid, comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample, which sample nucleic acid comprises a first        histone-associated nucleic acid species and a second        histone-associated nucleic acid species; and    -   (b) separating some or substantially all of the first        histone-associated nucleic acid species from the sample nucleic        acid, thereby generating a separation product enriched for the        second histone-associated nucleic acid species.

H2. The method of embodiment H1, comprising (c) analyzing nucleic acidin the separation product.

I1. A method which comprises analyzing nucleic acid in a separationproduct prepared by a process comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample, which sample nucleic acid comprises a first        histone-associated nucleic acid species and a second        histone-associated nucleic acid species; and    -   (b) separating some or substantially all of the first        histone-associated nucleic acid species from the sample nucleic        acid, thereby generating a separation product enriched for the        second histone-associated nucleic acid species.

I2. The method of any one of embodiments H1 to I1, comprising lysingvesicles present in the sample nucleic acid.

J1. The method of any one of embodiments F1 to I2, wherein separatingsome or substantially all of the first histone-associated nucleic acidspecies from the sample nucleic acid comprises contacting the samplenucleic acid with an agent that specifically binds to a histoneassociated with the first histone-associated nucleic acid species.

J2. The method of embodiment J1, wherein the agent specifically binds tohistone H3.3.

J3. The method of embodiment J1, wherein the agent specifically binds tohistone H1.

J3.1 The method of embodiment J3, wherein the histone H1 isunmethylated.

J4. The method of any one of embodiments J1 or J3.1, wherein generatingthe separation product comprises separating components bound by theagent away from the sample nucleic acid.

J4.1. The method of any one of embodiments J1 to J4, wherein the agentis an antibody.

J5. The method of any one of embodiments F1 to J4.1, wherein the samplenucleic acid is from blood plasma.

J6. The method of any one of embodiments F1 to J4.1, wherein the samplenucleic acid is from blood serum.

J7. The method of any one of embodiments F1 to J6, wherein obtaining thesample nucleic acid comprises subjecting the biological sample to an invitro process that isolates the sample nucleic acid from other samplecomponents.

J8. The method of any one of embodiments F1 to J7, wherein theseparation product comprises about 50% or greater secondhistone-associated nucleic acid species.

J9. The method of any one of embodiments F2, G1, H2, I1 and J1 to J8,wherein analyzing the nucleic acid in the separation product comprisessubjecting the nucleic acid to an in vitro sequencing process.

J10. The method of embodiment J9, wherein the sequencing processprovides sequence reads.

J11. The method of embodiment J10, comprising mapping the sequence readsto a reference sequence.

J12. The method of embodiment J11, comprising counting the sequencereads mapped to the reference sequence.

J13. The method of embodiment J12, wherein the counted sequence readsare utilized to generate an outcome determinative of the presence orabsence of a genetic variation.

J14. The method of embodiment J13, wherein the genetic variation is acopy number variation.

J15. The method of embodiment J13 or J14, wherein the genetic variationis a chromosome aneuploidy.

J16. The method of embodiment J15, wherein the chromosome aneuploidy isa chromosome 21 aneuploidy.

K1. A method for enriching fetal nucleic acid in sample nucleic acidthat includes fetal nucleic acid and maternal nucleic acid, comprising:

-   -   (a) obtaining cell-free circulating sample nucleic acid from a        biological sample from a pregnant female, which sample nucleic        acid comprises a first histone-associated nucleic acid species        and a second histone-associated nucleic acid species; and    -   (b) separating some or substantially all of the first        histone-associated nucleic acid species from the second        histone-associated nucleic acid species, thereby generating a        separation product enriched for the second histone-associated        nucleic acid species, wherein fetal nucleic acid in the        separation product is enriched relative to fetal nucleic acid in        the sample nucleic acid.

K2. The method of embodiment K1, comprising (c) analyzing nucleic acidin the separation product.

K3. The method of embodiment K1 or K2, wherein separating some orsubstantially all of the first histone-associated nucleic acid speciesfrom the second histone-associated nucleic acid species comprisescontacting the sample nucleic acid with an agent that specifically bindsto a histone associated with the first histone-associated nucleic acidspecies.

K4. The method of embodiment K1 or K2, wherein separating some orsubstantially all of the first histone-associated nucleic acid speciesfrom the second histone-associated nucleic acid species comprisescontacting the sample nucleic acid with an agent that specifically bindsto a histone associated with the second histone-associated nucleic acidspecies.

K5. The method of embodiment K3, wherein the agent specifically binds tohistone H1.

K6. The method of embodiment K3, wherein the agent specifically binds tohistone H1.0.

K7. The method of embodiment K4, wherein the agent specifically binds tohistone H1.1.

K8. The method of embodiment K4, wherein the agent specifically binds tohistone H1.3.

K9. The method of embodiment K4, wherein the agent specifically binds tohistone H1.5.

K10. The method of embodiment K3, wherein the agent is an antibody.

K11. The method of embodiment K4, wherein the agent is an antibody.

K12. The method of any one of embodiments K1 to K11, wherein the samplenucleic acid is from blood plasma.

K13. The method of any one of embodiments K1 to K12, wherein obtainingthe sample nucleic acid comprises subjecting the biological sample to anin vitro process that isolates the sample nucleic acid from other samplecomponents.

K14. The method of embodiment K13, wherein the in vitro processcomprises centrifugation.

K15. The method of any one of embodiments K1 to K14, wherein theseparation product comprises about 50% or greater secondhistone-associated nucleic acid species.

K16. The method of any one of embodiments K2 to K15, wherein analyzingnucleic acid in the separation product comprises use of a sequencingprocess.

K17. The method of any one of embodiments K2 to K16, comprising (d)determining the presence or absence of a genetic variation according tothe analysis in (c).

K18. The method of embodiment K17, wherein the genetic variation is achromosome aneuploidy.

K19. The method of embodiment K18, wherein the chromosome aneuploidy isa chromosome 21 aneuploidy.

The entirety of each patent, patent application, publication anddocument referenced herein hereby is incorporated by reference. Citationof the above patents, patent applications, publications and documents isnot an admission that any of the foregoing is pertinent prior art, nordoes it constitute any admission as to the contents or date of thesepublications or documents.

Modifications may be made to the foregoing without departing from thebasic aspects of the technology. Although the technology has beendescribed in substantial detail with reference to one or more specificembodiments, those of ordinary skill in the art will recognize thatchanges may be made to the embodiments specifically disclosed in thisapplication, yet these modifications and improvements are within thescope and spirit of the technology.

The technology illustratively described herein suitably may be practicedin the absence of any element(s) not specifically disclosed herein.Thus, for example, in each instance herein any of the terms“comprising,” “consisting essentially of,” and “consisting of” may bereplaced with either of the other two terms. The terms and expressionswhich have been employed are used as terms of description and not oflimitation, and use of such terms and expressions do not exclude anyequivalents of the features shown and described or portions thereof, andvarious modifications are possible within the scope of the technologyclaimed. The term “a” or “an” can refer to one of or a plurality of theelements it modifies (e.g., “a reagent” can mean one or more reagents)unless it is contextually clear either one of the elements or more thanone of the elements is described. The term “about” as used herein refersto a value within 10% of the underlying parameter (i.e., plus or minus10%), and use of the term “about” at the beginning of a string of valuesmodifies each of the values (i.e., “about 1, 2 and 3” refers to about 1,about 2 and about 3). For example, a weight of “about 100 grams” caninclude weights between 90 grams and 110 grams. Further, when a listingof values is described herein (e.g., about 50%, 60%, 70%, 80%, 85% or86%) the listing includes all intermediate and fractional values thereof(e.g., 54%, 85.4%). Thus, it should be understood that although thepresent technology has been specifically disclosed by representativeembodiments and optional features, modification and variation of theconcepts herein disclosed may be resorted to by those skilled in theart, and such modifications and variations are considered within thescope of this technology.

Certain embodiments of the technology are set forth in the claim(s) thatfollow(s).

What is claimed is:
 1. A method for enriching fetal nucleic acid insample nucleic acid that includes fetal nucleic acid and maternalnucleic acid, comprising: (a) obtaining cell-free circulating samplenucleic acid from a biological sample from a pregnant female, whichsample nucleic acid comprises a first histone-associated nucleic acidspecies and a second histone-associated nucleic acid species; and (b)separating some or substantially all of the first histone-associatednucleic acid species from the second histone-associated nucleic acidspecies, thereby generating a separation product enriched for the secondhistone-associated nucleic acid species, wherein fetal nucleic acid inthe separation product is enriched relative to fetal nucleic acid in thesample nucleic acid.